Puella Magi Madoka Magica/Fanfic Recs

Proof that the remaining 10% is worth making a wish for here. /人 ◕ ‿‿ ◕ 人\

These are recommendations made by Tropers for Puella Magi Madoka Magica fanfics, all of which have to be signed to stay on the page. Feel free to add a fanfic of your own to the list, but remember to use the template found here.

You can also add to the current recommendations if you want. Refrain from posting Conversation in the Main Page though; that goes in the discussion page. No-name recommendations will be Zapped. Nobody would back up the rec. Discussion of the recommendation is welcome on the discussion page. As such discussion is important, do remember to add the discussion page to the watchlist, if need be.

Do warn when a fanfic may head into non-canon territory. Some people just don't like it, and as we all know, Shipping is Serious Business.

General Fics
The Second Law of Thermodynamics by TheEdwardz
 * Recommended by User:Animenutcase
 * Synopsis: Kyubey reflects on the universe and explains the circumstances behind the events of the original timeline. Some science stuff.
 * Comments: The "science stuff" in the synopsis isn't kidding. Very rarely does one find a fic that has been clearly well-researched. It also contains a lot of speculation on as well as Mami's relationship with her parents. But best of all is Kyubey's narration. He may not, but damned if he isn't willing to try using it against us. He goes so far as to accuse humanity of being hypocrites because we call him evil when he , and at the same time giving the impression that he's addressing the reader directly. It's a fantastic read and really helps me see Kyubey as an entertaining villain. I should warn you: It contains spoilers for up to episode 10 - and this is a series that churns out Wham Episodes like butter.

Magica Musical by angel0wonder
 * Recommended by User:F 1 zzyp 0 p
 * Synopsis: Exactly as it says on the tin, it features lyrics to 4 different scenes in the show.
 * Comments: Just TRY to not crack a smirk after reading the first song and it's conclusion plus the ever so stoic Homura dropping a beat of all things...Hilarity Ensues.

What A Human Can Do by Opt281
 * Recommended by User:Psyga 315 and the User:Ace Of Scarabs
 * Synopsis: The story of a young man, a time loop, and the secret world that he discovers while trying to escape it.
 * Comments: The story is mostly about the young man investigating and slowly finding out about the secret world of the Magical Girl  and the ensuing hilarity and drama that comes from it. This is a great story that shows that Original Characters can be interesting when done right. I do warn that it does contain spoilers for up to episode ten, . Also, there is some OCxYellow shipping.

Puella Magi Homura Magica by Lestaki
 * Recommended by deathcurse, User:A Bad Driver, Grand Prince Paul II, enviroguy, asellus111
 * Pairing: Homura/Kyoko
 * Synopsis: Living in the world Madoka's sacrifice created, Homura, Mami and Kyouko uneasily coexist while fighting the demons of Mitakihara Town. But as the miasma thickens and the demons multiply, the fragile peace of their lives threatens to shatter once more.
 * Comments: It's a great Continuation Fic about Homura, Mami, Kyouko and fighting demons as a team while new threats and new conflicts arise.
 * Several OCs are introduced over the course of the story, but they are fairly strong and likable characters in their own right.
 * The OCs can seem to overshadow the canon characters at times, however.

Magica Madoka Veneficus Puella by The Moiderah of Writing
 * Recomended by User:dalekandrews, enviroguy
 * Synopsis: A single wish. That's all it took. When Madoka's final wish changes everything, Homura's powers disappear, and apparently, the world is safe. However, the Witches still exist, and now, they're even more powerful than ever. Kyubey still lives, after all.
 * Comments: After in the current timeline, Madoka decides to become a Puella Magi, wishing for a world where her friends would survive. Not only does this remove Homura's Time Travel powers (without diminishing her Badassery), it changes the whole setting. Now not only are witches and magical girls -now called Veneficus Puella- more powerful than before, now the Muggles are aware of the whole thing, making matters even more complicated for our heroines.

Thanks☆Kyubey by Gakubuchi Aiko
 * Recommended by User:Sonic GTR A Bad Driver
 * Synopsis: Kyubey uses the honey over vinegar approach to carry out his mission by being completely honest with the girls and being a pretty nice Weasel Mascot. Girls Love.
 * Or: In a world where Kyubey is completely honest, forthcoming with information, and friendly...
 * Comments: The story mostly follows the series and was finished before Episode 10 which is why there is nothing regarding . While it is a Lighter and Softer take on the series and ends on a high note, there's still room for tragedy. Look out for the Art Shift.
 * Warning: This doujin is on Danbooru, meaning the usual warnings about NSFW ads apply.
 * A trope page under construction

I'm working at a mahou shoujo recruitment company, but I think I may be at my limit by Momiji Mao
 * Recommended by Two Gun Angel, A Bad Driver, and User:Psyga 315
 * Synopsis: Kyubey is a mahou shoujo recruiter who is seriously down on his luck, such that his boss is threatening him with termination if he continues to drag down the company. With no one but his wife and his friend in the company supporting him, Kyubey may be at his limit...
 * Comments: This twenty-page doujin, one of the Pixiv 1000 collection, is one of the few fics that manage to humanize Kyubey (as humanizing as you can get for a Starfish Alien, anyway) and even get us to root for him. What at first looks like a Slice of Life office fic soon turns into a superb Start of Darkness for our little Weasel Mascot. Note that it also has the dubious honor of having Kyubey look for a "quota".
 * Warning: This doujin is on Danbooru, meaning the usual warnings about NSFW ads apply.

A History of Magic by Danny Barefoot
 * Recommended by User:biichan, enviroguy, the User:Ace Of Scarabs, Constantly Comic, User:Animenutcase
 * Synopsis: The stories of Magical Girls throughout history who contracted with Kyubey, and their fates. Inspired by Kyubey's history lesson in ep 11.
 * Comments: Interesting, well-written historical fiction. Stories for, , , and , along with several others, are up as of the writing of this rec, with more promised to follow.
 * Also some stories about such women as Alice Liddel and Nimue. All the chapters, regardless of subject matter, are believable, entertaining, and historically accurate.
 * Ace: The stories shed some horrifying new insights into the possible histories of mankind, if the Incubators were really amongst us. Danny pulls no punches with the historical girls, all the way back.
 * Constantly Comic: Extremely well-written. The various girls are all really easy to become attached to, making for some real Tear Jerkers. The ending is beautiful and nearly brought me to tears.

Optimal Outcome by Michael Saniyan
 * Recommended by enviroguy, Grand Prince Paul II, and A Bad Driver
 * Status: Complete
 * Shipping: One-sided (probably) Homura/Madoka, Kyouko/Sayaka,
 * Synopsis: Kyouko is a teacher with Homura as her closest friend. Madoka spends more time with Mami than with anyone else. Sayaka is neglecting normal life in general and Hitomi is struggling with a dead-end relationship. Witches aren't exactly top priority anymore.
 * Comments: Some spoilers for up to episode 10. Mami is not killed by Charlotte but taken out of commission, and Kyouko accepts a deal with Homura to teach Sayaka how to fight. Kyouko and Homura become better friends and pursue their respective love interests. All well and good, except that Charlotte defeating Mami involved breaking off a piece of her soul, driving her to depression and mental instability.  An interesting premise and very well-written. Everyone's more-or-less in character and when they're not (Mami) it's justified by the events of the story. A number of good twists over the course of the story.
 * And now the author has published the sequel, Perpetual Probability.

HomuHomu's Grand Strategy by norabako8
 * Recommended by User:Gunbazca and A Bad Driver
 * Synopsis: After n iterations, Homura starts to think on how to win from Walpurgisnacht.
 * Comments: Presents an amusing take on Homura's strategy to beat Walpurgisnacht without resorting to Madoka's intervention. Starting with eliminating Sayaka from the game, but it doesn't change a thing. Ends with . Also a Pixiv 1000.
 * It's hosted in danbooru so watch out for those NSFW ads!

Never Ending by hirotasyou
 * Recommended by User:kwsn, totlmstr
 * Synopsis: Homura finally manages to defeat Walpurgisnacht, but something isn't right...
 * Comments: The biggest witch of all time is dead. However, Homura finds out exactly what her contract, and more importantly her wish, entails.
 * It's hosted in danbooru so NSFW ads! Also spoilers for the last few eps. And, finally, it's very dark. Consider yourself warned.

Episode 12 by tugeneko
 * Recommended by User:Gunbazca
 * Synopsis: Aptly Named. This is what Episode 12 would have been if tugeneko took the reins from Gen Urobuchi. Crackier than Urobuchi. A bit NSFW, too, if in idea form and not drawing.
 * Comments: There's really not much words to describe this doujinshi. This is what will happen if Madokami would give Refuge in Audacity a form it would share with Hilarity Ensues. Homura in this doujin is extra-perverted. The drawing style is very simplistic, but funny enough. Ends with.
 * It's hosted in danbooru so watch out for those NSFW ads!

The Disappearance of Miki Sayaka by Aku-dono
 * Recommended by User:A Bad Driver and User:Psyga 315
 * Synopsis: Miki Sayaka's mysterious disappearance draws more than a few questions from her mother. Takes place after episode 12.
 * Comments: This fic really goes into the details and aftermath of what happened with Sayaka's parents, even deconstructing their efforts to find her. Be warned, it is very dark.
 * As in What A Human Can Do and As Time Diverges, this includes an investigation element, but this time

Charlotte's Life Before She Turns Into A Witch
 * Recommended by Teslashark
 * Synopsis: A girl with cancer met QB in hospital...
 * Comments: Filled with Tear Jerker, comerades. This work suggests that the "Minnie Worm" that ate Mami is made of cancerous cells, and Charlotte is innocent.

Magia Revolution by /a/nonymous magica
 * Recommended by Malagasy Parrot, the User:Ace Of Scarabs, and User:Psyga 315
 * Synopsis: Take Madoka Kaname from the main timeline of the anime, and hand control of her body to the anonymous folks at /a/. The same anonymous folks who have watched the show.
 * Comments: Basically a series of (now archived) Choose Your Own Adventure games from 4chan's /a/nime and m/a/nga board that raises an interesting question: What If the mind of innocent little Madoka is swapped with that of /a/'s collective consciousness, turning her physical form into a Genre Savvy crusader who seeks to set things right? Uncontrollable plot points from the show remain present, but the actual plot diverges drastically as a result of game breaking decision making and abilities courtesy of Anonymous. This is not without complications; meddling of the timeline has led to, among others, . The series started out very lightheartedly (by lighthearted, we mean Anonymous-controlled Madoka being hilariously out of character on the first day) before drifting in and out of Serious Business territory. It doesn't hold back with the MadoHomu shipping either.
 * Ace of Scarabs: Despite the disruptive mental presence of Anonymous in the PMMM timeline, the story manages to assert itself and draw the hivemind into it in a most amusing and heartbreaking way. The Genre Savvy of the Anonymous collective adds to the entertainment value as various facets of the hivemind immediately panic at the slightest hints of Death Flags going up. Even more amusing is how the story-writer paraphrases Gen Urobuchi by claiming that they wish to be a "healing-type" writer.
 * Psyga315: It's funny to see people going Oh Crap over the slightest thing (For example, people freaked out over "All seemed well") and try to get the best ending possible despite the fact that this is Madoka Magica we're talking about. It's so frantic that it's funny. To see this in action, see episode 11. One problem is that late in the series, there has been so many spam attacks. And the spams are usually very NSFW.

Reckless Girl Sayaka Sowaka by abua
 * Recommended by Gunbazca
 * Synopsis: Sayaka discovers that she can morph her soul gem into a mini-me. Hilarity Ensues from there.
 * Comments: Where to start? This manga is a gag manga, dealing with some episodes of the original work in a different tangent. Highlights include Mini-Sayaka, dead bodies in front of Kyosuke's door, misunderstandings, general absurdity, near the end. I wish I'm joking. However, some pages are not fully translated. Also, this is danbooru-hosted so watch those NSFW ads!

''[http://www.mspaforums.com/showthread.php?39168-Aisleventure-Make-a-contract-with-me-and-become-a-magical-girl!-THE-END Make a contract with me and become a magical girl! The Aisleventure]'' by User:Brickman
 * Recommended by Canonier
 * Synopsis: Apparently a Choose Your Own Adventure about a Puella Magi played by some posters on a forum dedicated to !!MS Paint Adventures ...?
 * Less a Choose Your Own Adventure and more a fusion between Madoka and the traditional "Jackass Genie" game, with most wishes resulting in humorous short stories and some vague continuity arising later on. Some even manage to get happy endings. -User:Brickman

The Happy Ending I Made Up by kuragemodoki
 * Recommended by User:Jake Was Here
 * Synopsis: Six years after the end of the series, Kaname Tatsuya is becoming curious about his neighbors Homura and Kyuubey, and the sister that they say he once had.
 * Comments: Starts off slow, with a few yonkoma gags about Tatsuya's friendship with Homura, but takes off in a completely different direction once it's revealed that he knows Kyuubey and still hasn't forgotten Madoka. In the process, it manages to tie up a number of loose ends from the series and plug a bunch of Plot Holes that I didn't even realize existed until took advantage of them. The last four pages or so are the comic's Crowning Moment of Awesome -- completely heartwarming and very true to the characters. (NSFW warning: Hosted by Danbooru)

To The Stars by Hieronym
 * Recommended by Sackett, asellus111
 * Synopsis: Based on the glimpses of the new world we see in the last episode. Fast forward several hundred years and humanity has spread across the stars.
 * Comments: Incredible world building, and great to see Mami and Kyouko again. Mami is still being Mami, and Kyouko is preaching the good news. Homura is mysteriously absent...
 * Comments: As one of a very few distant future take on how the Puella Magi system might evolve, it is probably one of the best, with a setting that is both recognizably in the Madoka-verse, yet uniquely different.
 * Has a page.

The Shrine, by Shadowheartdesigns
 * Recommended by User:Fringe Benefits
 * Synopsis: The story of a simple shrine constructed to honor the Goddess, and its mysterious visitors.
 * Comments: This is a very short but incredibly awesome little story, and it presents an intriguing possibility that Madoka isn't quite as gone from the new world as you might think. It's very sad but very touching, and it gave this troper goosebumps.

Demon Cleaners by FourthWall
 * Recommended by Cheeseand Cake
 * Synopsis: Post-episode twelve, Sayaka and an avatar of Madoka reappear proclaiming themselves Demon Cleaners MIKI and KANAME in capital letters and dramatic fashion. But there's the little question of just who wished them back? Especially in Madoka's case. There also appears to be a Demon King of some kind hatching beneath the school.
 * Comments: It hasn't gotten too far along yet, but the writing's solid and the humor is certain to make you crack a grin.

Times Like These by dear future
 * Recommended by obstinateRixatrix and Grand Prince Paul II
 * Synopsis: Even in a world without magic, where there are no miracles to light the way out of the darkness of despair, everything balances itself out.
 * Comments: A oneshot taking a look at the lives of the Puella Magi girls if Kyubey didn't exist to screw them over. It is very much worth the read!

Roleplay Puella Game Madoka Magica by Person With Many Aliases
 * Recommended by TSB
 * Synopsis: Alright guys, I think it's time you took a break from the doom and gloom and had something a little more lighthearted. "No!" She shouted back, frustrated, "Not yet! I just need a few more minutes! This raid won't last without my help!"
 * Comments: I found the writing a bit weak in places, but the overall concept is so hilarious that I was laughing anyway. All of the magical girls' personalities and quirks are translated brilliantly into gamer archetypes. I was sold on this fic when it described Madoka as the kind of girl who doesn't understand the difference between gaming and playing Bejeweled on her phone.

MadoMagi Panic by Colonel Aki
 * Recommended by Sachiko
 * Synopsis: The author of Touhou 4koma Long Runner Life of Maid tackles Madoka Magica. Hilarity Ensues.
 * Comments: This series of 4komas follows the storyline of the anime, but with a hilarious, slapstick comedy twist. It's short, but seeing the shenanigans of Madoka and company will keep you entertained for a while. Oh, and Kyubey is a masochist.

Resonance Days by Taker Foxx (also has a spacebattles thread)
 * Recommended by Madan Eccles 19 and Grand Prince Paul II
 * Synopsis: Falling their mutual demise at each other's hands, Kyoko and Sayaka wake up in a strange world. Now, with Kyoko's soul gem missing and Sayaka's humanity and personality only partially restored, they must band together to survive.
 * Comments: The synop doesn't do this story justice, at only three chapters it's already looking to be a wild ride.

Shipping Fics
A Happy Dream by angel0wonder
 * Recommended by User:Epic Fighting Troper, asellus111, User:Ultimate Chimera, enviroguy, Sachiko, Taker Foxx
 * Pairing: Kyouko/Sayaka
 * Synopsis: A AU Fic where where the Magical Girl system does not exist, but our two lead's problems still do. The homeless Kyouko moves in with the more well-off Sayaka and becomes Vitriolic Best Buds with her... and maybe something more.
 * Comments: Hands down, if you are in any way a fan of the KyouSaya pairing, you just HAVE to read this. It's cute, funny, heartwarming, with a side order of tease and a whole lotta heart. All the character's personalities are perfectly nailed down here (No OOC here, ladies and gentlemen!), and the interactions between the two leads are absolutely hilarious. A MUST READ.
 * Sachiko: It is also full of Shout Outs to the original series, some of them incredibly funny, some awe-inspiring. They all just fit in a way that can be even frightening. And seeing Kyoko and Sayaka's personalities clash one moment, then open to each other little by little at another moment can bring one to tears. If Madoka Magica was turned into a slice of life, I'm sure it would look at least a bit like this fic, so if you like that kind of stories and liked Madoka Magica, you must read it, no excuses.

Anything Worth Doing Is Worth Doing Badly by ZipCode
 * Recommended by User:Comartemis, enviroguy
 * Pairing: Homura/Kyouko
 * Synopsis: Homura wakes up in a world where the only witch is the one in her head.
 * Comments: Kyubey, the Witches, and the Puella Magi are all gone. The good guys won, and everyone gets to live "normally" in a new timeline. Now What?? Everyone lives Happily Ever After? Turns out it's not quite that simple, especially not for Homura and Kyouko.
 * Rather dark, but very powerful. This story has a very believable take on how Homura would be affected by the repeated timelines and trials (in this fic, over 400 of them), and the trouble she would have adjusting to regular life afterwards. The characterization is great, with only one notable occurrence of Out of Character on Sayaka's part (which many considered justified or at least believable). Kyouko's life has been changed a lot in this world, but she still fits in rather well with canon characterization.

Heaven Is A Zombie Apocalypse by ZipCode
 * Recommended by User:Comartemis, enviroguy
 * Pairing: Kyouko/Sayaka
 * Synopsis: Kyouko and Sayaka wake up alive and in one piece. The question is how, why, and why the heck has Mitakihara become a Ghost Town?
 * Comments: Starts off with fluff and shipping goodness, gains a touch of psychological horror later on.

The Only Constant by Raiyo
 * Recommended by User:Robotic Skies
 * Paring: Slight Homura/Madoka
 * Synopsis: Just because everything is different doesn't mean anything has changed. Homura as she tries to keep her world from falling apart again and again. Spoilers. Character death.
 * Comments: This is a story written very early into the fandom before ending or many plot related episodes had aired and, as such, is no longer canon. However, I really love the emotion displayed in this piece and find it to be done quite well.

Good night, Homura-chan by hijikini
 * Recommended by User:Andyzero
 * Pairing: Madoka/Homura
 * Synopsis: Homura walked a long road to protect what Madoka left to her. Like all paths, it has an end.
 * Comments: A danbooru doujinshi. It takes place with full spoilers of the last episode. NSFW ads warning.

Last Episode of KyouSaya by Kodou Mikoto
 * Recommended by User:Andyzero
 * Pairing: Kyouko/Sayaka
 * Synopsis: Goddess Madoka comes for all magical girls in the end.
 * Comments: A danbooru doujinshi so watch out for the NSFW ads.

If Only She were A Little Closer by kamereon
 * Recommended by User:Gunbazca
 * Pairing: Kyousuke/Sayaka
 * Synopsis: Hitomi did confessed something to Kyousuke, but it's a little different...
 * Comments: Not a long one, but it does paint a better picture of Kyousuke, and turns out that he's not so bull-headed after all. Quite a heartwarming moment at the end, too... and what is more satisfying than to spite Kyubey while we're at it?
 * It's hosted in danbooru so watch out for those NSFW ads!zz

Alea Jacta Est/MadoHomu Manga Love Means Never Having To Say You're Sorry/KyouSaya Manga, Feels Like We Met Each Other In A Past Life/MamiyaCharlotte Manga, The World Is Waiting For Sunrise/QB Personification Manga, A Colorless Crow/ Older Tatsuya Manga by kurono yuu
 * Recommended by User:Gunbazca, User:Ultimate Chimera
 * Pairing: male!Madoka/Homura, male!Kyouko/Sayaka, non-romantic male!Mami/male!Charlotte
 * Synopsis: If half the cast were male, what would change? A male Madoka confesses to Homura, an ironically-named male Kyouko is able to get through to , and a male Mami and male Charlotte chat about how they impact each others lives in the afterlife. But what's happened to our favorite Incubator, now in human guise, after everyone left and they reached their quota...? And what about Tatsuya, growing up able to see a brother that nobody else knows exists?
 * Comments: Heavy Alternate Universe, but stays relatively faithful to the original. The first comic between Madoka and Homura is arguably more heartwrenching than the original, as the two confess their love as . In the second comic, Kyouko is now named Kyousuke, and . Makes a bit of 'the other Kyousuke' joke near the beginning, but gets more and more heartwarming towards the end. The third comic features "Mamiya" and "Char" showing that even if they forget each other, brotherly love can transcend lifetimes. The fourth comic tells us the story of Kyubey leaving Earth, only for flashes of a person who never existed to come into his memories. The fifth takes place some years after the anime's finale, with Tatsuya as an isolated middle school student due to his ability to still see Madoka. The art style is fantastic, and even if you're not a fan of genderbends or these sort of pairings, it's well worth a read. If you doubt these comics' quality, it's worth knowing that these manga are currently Pixiv 1000, meaning it's bookmarked by over 1000 Pixiv members.
 * It's hosted in danbooru so watch out for those NSFW ads!
 * Now with an English fandub.

Mami-san Manga by usakiyo
 * Recommended by User:Gunbazca
 * Pairing: Mami/Homura
 * Synopsis: Homura managed to recover Mami's Soul Gem, which turns out to be undamaged by Mami Mogu Mogu. Mami recovers, but Homura asks a favor out of her.
 * Comments: Another Alternate Universe piece, which is similar to something I remember reading in the WMG here somewhere first. Very short, but contains quite a lot of text; I'm not sure if there's really any Homu/Mami shipping involved, but Mami does flirt with Homura a bit. Another Pixiv 1000 entry, so don't worry about the quality.
 * It's hosted in danbooru so watch out for those NSFW ads!

Have Your Death And Eat Cake Too by SailorPtah
 * Recommended by User:fishsicles
 * Pairings: Madoka/Homura, Kyouko/Sayaka, Madoka/Harem, a bit of Mami/Charlotte
 * Synopsis: An examination of . Written from the prompt "Madoka's magical girl harem".
 * Comments:
 * fishsicles: Well-written and entertaining, even if you are not that much of a shipper. One of the best among the many fics that aim to turn the (arguable) Esoteric Happy Ending into a genuine one, and by my estimation succeeds.

A Brand New Day by ShadowKittenMewFan
 * Recommended by enviroguy, Grand Prince Paul II
 * Pairings: Homura/Sayaka, hints of Homura/Mami, Homura/Kyouko, Kyouko/Sayaka
 * Status: Complete
 * Synopsis: Madoka's Wish changed the universe. Broke the system. Gave everyone a new chance. What will life hold for Homura in a world without Puellae Magi, or Witches ... or Incubators? A very AU story in an alternate post-series time-line.
 * Comments:
 * The best Homura/Sayaka multi-chapter fanfic on FF.net, and notable for actually making the pairing work believably and enjoyably with both in-character, despite all the canon evidence against this possibility. Very character-driven, and a nice look at how everyone would interact in a non-magical setting.

Broken Rose by Danny Barefoot
 * Recommended by enviroguy
 * Pairings: Kyouko/Sayaka
 * Status: In-progress
 * Synopsis: Throughout many timelines, their distance remains the same.
 * Comments:
 * An excellent look at how Kyouko and Sayaka, as well as the other Puellae Magi, might have interacted over a dozen timelines. Places more evidence on Kyouko's past than most fics, and really plays up the Not So Different dynamic between her and Sayaka, given all of the different scenarios they are placed in. Doesn't really get serious with the shipping until the last few chapters. All of the characters are portrayed very believably and in-character. Definitely worth a read, especially for fans of either character or the ship itself.

Crossover Fics
Puella Magi Madoka Magica In by ZipCode
 * Recommended by User:A Bad Driver, enviroguy
 * Synopsis: A set of crossover drabbles. Different crossover per chapter. Mostly crack. Lots of yuri.
 * Comments: "Mostly Crack. Lots Of Yuri." Yeah, he wasn't kidding. A hilarious departure from the original plot...which is to say little to no relation with the original plot at all, save for a few Take Thats to Kyuubey. Thankfully, there are very few spoilers, but there are a few Mythology Gags in each crossover, so watch out.

A Hero by Bioweapon 155
 * Recommended by dalekandrews, Comartemis, A Bad Driver
 * Crossing over with: Doctor Who
 * Synopsis: Heroes can come from the most unlikely of places. And what is more unlikely than a Dalek trying to resurrect his dead race?
 * Coments: Dalek Sec inexplicably survives his death in Daleks in Manhattan (somehow negating the whole Half-Human Hybrid thing along the way), and ends up tracking Homura's shield through Mitakihara.
 * Comartemis: There is nothing in the world that is quite as sweet as a Dalek talking morals with an Incubator, declaring their methods to be repulsive, and meaning it without a trace of irony. If you despise the Incubators and would love to see QB's Omniscient Morality License shoved back down his throat, I guarantee you that Sec is going to be your new best friend.
 * WARNING: This story will make you root for the Daleks. You have been warned.

Lyrical Chronicles by velsper56
 * Recommended by: User:dalekandrews
 * Crossing over with: Magical Girl Lyrical Nanoha, Magic Knight Rayearth and some Super Robot Wars
 * Synopsis: Precia Testarossa's use of the Jewel Seeds causes more damage to the dimensional walls surrounding Earth than anyone could've expected. Now magical girls from across time and space have gathered. Forging new allegiances and battling new foes. Set up. Go!
 * Coments: A supposedly dead Mami Tomoe and Homura Akemi End up in the Nanohaverse's Earth after the whole Jewel Seed crisis happens. Mami's soul merges with Alisa Bannings. Nanoha blows up witches. Homura becomes a different sort of magical girl through a Journey to the Center of the Mind. Both of them become even more badass. Alternate Spacebattles link is here.
 * Currently being rewritten here.

Paved with the best intentions by Zipcode
 * Recommended by: User:dalekandrews
 * Crossing over with: Magical Girl Lyrical Nanoha.
 * Synopsis: None.
 * Comments: A very weird welding of both Nanoha and Puella Magi canon. Written by Zipcode, so it's well worth the read.

There's Nothing to Be Afraid Of We Live On As One Let's Go, My Friends by rokudena-shi
 * Recommended by: Darth
 * Crossing over with: Tengen Toppa Gurren Lagann.
 * Synopsis: A trio of comics by Pixiv artist rokudena-shi parodying three of Gurren Lagann's most iconic scenes.
 * Comments: Have recently become quite pertinent in light of Madoka Magica's final episode. They have been translated into English for the most part, but the panels that haven't aren't all that hard to understand anyway. Fans of both series are sure to get a good kick out of them.
 * Warning: Some site ads are NSFW.
 * Comartemis: If you despised the suffocating cynicism and the Downer Ending of the canon series, then all three of these comics are an absolute must-read. Row row fight the powah, girls.

As Time Diverges: The Mitakihara Case by NaXyld
 * Recommended by: TheNerfGuy and User:Psyga 315
 * Crossing over with: Death Note
 * Synopsis: SPOILERS! Within The time loop... a small detail changed. This small detail caused two young men, who might have been mortal enemies, to instead become allies. And the key to the truth of the Incubator might not be a Puella Magi or a witch... it could be them.
 * Comments: This story has the potential to be very good. Well written, suspenseful, catches the themes of both fandoms. The author is providing the right warnings too. The only thing that could ruin it is the lone continuity error and even that might not do much against the fic.
 * It also provides the same "mystery" element from What A Human Can Do and contains a good L/Light relationship in which they are working together, rather than against each other.

Puella Magi Amelia Magica by Melengro
 * Recommended by User:biichan
 * Crossing over with: Doctor Who
 * Synopsis: In which Incubator gets his paws on Amy. Because Eleven didn’t come back…
 * Comments: Is it wrong to rec something you convinced someone to write? Because this is really good. It takes a depressing premise, turns it into something absolutely heartbreaking, and the last line is the wham ending to end all wham endings. Plus, we get witch card text for.

I've Managed to Save Mami-san by nemo (nameless920).
 * Recommended by User:Gunbazca, Vrock 8, Grand Prince Paul II
 * Crossing over with: Berserk
 * Synopsis: Guess who showed up as Mami Mogu Mogu is about to happen? Hint: He wields a large sword.
 * Comments: Very short and contains very little text, but still managed to be a heart-pounding CMoA in which . It's also drawn in styles resembling the original Berserk, so Guts is not moe-fied. A fun and uplifting little read.
 * It gets a Hilarious in Hindsight when the dub of Madoka is announced, and Mami's dub voice did.
 * It's hosted in danbooru so watch out for those NSFW ads!

 by ねも
 * Crossing over with: Berserk again.
 * Synopsis: Every little girl's favorite aloof big brother figure helps Sayaka out.
 * Comments: Short and simple: Sayaka gets some sense talked into her. Oh, how I wish this wasn't a fanfic...

 by ねも
 * Crossing over with: Berserk. Seems like an obsession. But it is so cool...
 * Synopsis: Now it is Kyouko.

God, by linkhyrule5
 * Recommended by Comartemis, enviroguy
 * Crossover with: Touhou
 * Synopsis: Madoka was prepared to spend eternity fighting witches. She was somewhat less prepared for what being a sentient concept actually entailed. The good news is, there's people who can show her the ropes for that sort of thing. The somewhat-less good news is, the one she's got is everyone's favorite boundary manipulator. And Reimu's already getting a headache from this one.
 * Comments: Takes place post-series, obviously. LH5 has some interesting ways of visualizing Madoka's existence as a sentient concept, the downside to which is that you need to follow along rather closely at first or risk suffering a Mind Screw.

Stars Above, by Fringe Benefits and Forzare
 * Recommended by hyperderpy
 * Crossover with: Lucky Star
 * Synopsis: Homura crosses timelines to transfer into Kagami's class in Ryouou High, in order to protect the Hiiragi sisters from a multidimensional threat... one that's already destroyed one universe.
 * Comments: Revising my earlier comments: This is much, much more than a mere "shipping fic". What's being done in Stars Above is a real, honest-to-God epic crossover. The authors clearly understand the important themes of both series, and care deeply about both sets of characters. They're doing a great job of contrasting the two worlds, and playing the differences in interesting ways. Special mention also goes to the fight scenes, which are awesomely epic and creepy in the same way the Witch battles were in Madoka. Highly recommended!

The Many Lifes Of Mami Tomoe, by Sheo Darren
 * Recommended by R Bomber
 * Crossover with: Ghost Rider, Fate/stay night, Kore wa Zombie Desu ka?, Guyver, Stardust Witch Meruru, Takamachi Nanoha of 2814, Lyrical Nanoha (yes, the original), Ultimate Girls, Alan Scott's Green Lantern.
 * Synopsis: Kyubey is not the only entity out there that can grant a second shot at life. What if someone else beat him to Mami? Everything turns upside down, that's what.
 * Comments: A What If story, when Mami Tomoe receiving power from another entities other than Kyubey. An utter Crack Fic, featuring different world every single chapter. Sheo Darren aware of this wiki, so expect Shout-Out, a lot of them. Also incorporates some other series (which isn't listed here, since they usually only Shout-Out). If you want a good laugh, or just too depressed after watching Puella Magi Madoka Magica, this is a good read. Oh yeah, last chapter was kinda long and more serious than other chapters, so you've been warned. But it is also had good stories.