Princess Tutu/WMG

Princess tutu is related to Mytho in someway.
Inspired by a fanfic. Princess Tutu seems to share Mytho's white hair, if Ahiru's Princess Tutu form is any indication. Admittedly, this could also be a side-effect of using Mytho's heartshard to transform, but none of the people in possession of heartshards have shown such a side-effect.
 * That white, feathery stuff covering her ears? Yeah, that's not hair. It comes from the costume of Odette from the Swan Lake ballet. It's especially obvious in this picture, after you've looked at the last one.
 * Alright, that makes sense. I still think it looks like hair, but it's probably just the art style. What's with the fade into white with her ahoge, though?

Fakir and Rue are siblings.
Fakir's mother--shown in a brief flashback in episode 20--looks remarkably similar to Rue (for being seen only in shadow, anyway). Also, on Autor's family tree, the person that he identifies as Fakir on the tree has a sibling...that's been crossed out. Rue was kidnapped by her family as a baby, and so doesn't remember what they were like. Fakir has suppressed most of the memories before his parents died, and he and Rue are also close in age, so if she is his sister it makes sense why he wouldn't recall her. Also, if you compare how the two looked as children, they appear very similar. (Although, admittedly, it could just be due to the art style.) As one last final interesting tidbit, Fakir appears briefly in the background of Rue's flashback of her childhood when the story goes backwards in episode 23--you can see him fighting attempting to fight off crows with a toy sword to save a small animal (possibly a cat). Plus, don't they just ACT like siblings fighting over a favorite toy?

Autor actually is a descendant of Drosselmeyer.
He's the first one in akt 23 to realize that the story is going backwards--Fakir has to ask him what's going on, and Drosselmeyer seems (pleasantly) surprised by the story going backwards, as if it's never happened before. If it hasn't happened before, then Autor couldn't know about it through research alone--in actuality he can sometimes hear the story being told because of the vague bits of Drosselmeyer's DNA that's in his blood. This also means that his claim that he heard the Oak Tree sigh is actually true. (Probably it was sighing in exasperation from how insane the kid tapping into her roots is.) However, he's too distant of a descendant to be able to control a story through pen and ink--he's cursed to be able to hear the words of Story Spinners, but never truly become one himself. Or, alternatively...

Autor's too logical to be a writer and use the Story-Spinning powers.
Perhaps he does have the potential to use the powers, but he's so fond of logic and formulas ("blue and black ink at a 7/3 ratio", "Drosselmeyer's special blend of tea--three parts Darjeeling and then added Assaam"...) that he can't understand the creative process. (Similar to how Drosselmeyer tells Fakir that he has to "let go and be irresponsible with your writing.") It's not that he doesn't have the right bloodline, he's just not a talented writer. At all.

Ahiru/Duck is a character Fakir wrote in a story as a child.
Think about it: Fakir is obviously fond of animals. As a child, one of Fakir's stories was about a little duckling with a big heart and the mind of a human girl. Since he wrote her as a "duckling" she was never able to grow older, but with the mind of a little girl she was able to mentally and emotionally mature to the age she appears as in the show. This is one of the reasons why Fakir can write about Ahiru, and why Drosselmeyer has such a difficult time controlling her--she's Fakir's character, not Drosselmeyer's. Tutu, however, is Drosselmeyer's character. This means that the girl Ahiru is a character shared between the two. (And also why Fakir has to call out her true name, and not "Princess Tutu"--he has no power or right to call one of Drosselmeyer's characters out from his realm.)

Autor and Malen are brother and sister.
Not my theory, but one that I've seen appear in a few fanfics. The general logic probably stems from the fact that they have glasses and similar hairstyles, both are attracted to/obsessed with Rue, and they both throw themselves wholeheartedly into their passions.
 * This would explain why in the epilogue he's telling her to be quiet.

Lilie is Drosselmeyer's true sucessor.
Either another one of his descendants, or simply his spiritual successor chosen to highlight the tragedy of the story. Autor isn't creative enough and Fakir isn't sadistic enough to be considered worthy by Drosselmeyer. Sadly for Lilie, Drosselmeyer was unable to contact her to carry out his will before Fakir finished his story.

Edel is made from the wood of The Great Oak Tree.
Not my theory--thought up by Tomoyo on the LiveJournal community. Notable because this was confirmed by Word of God at the Princess Tutu Cast Party held at Ushicon. This is why Edel and the Oak Tree repeat similar phrases.

Haruhi Suzumiya is a descendant of Drosselmeyer, possibly through Fakir.
Or Kyon, depending on if you believe the theory in Haruhi's WMG. This is the source of her reality-bending powers--although, of course, she's a prodigy that has refined the Story-Spinning powers beyond the level that Drosselmeyer and Fakir reached. She no longer even needs a pen and paper to use her powers!

The novelist in Stranger Than Fiction is a descendant of Drosselmeyer.
Pretty straight-forward. Drosselmeyer writes tragedies that become reality until his characters rebel. Karen Eiffel is a writer of tragedies that become reality until one of her main characters contacts her and asks her to not kill him. Of course, Karen isn't nearly as cruel as Drosselmeyer--a descendant that Drosselmeyer would probably be disappointed in.

Autor's father trained him to be a Story-Spinner since he was a young child.
Autor is careful to note that one of the Story Spinners on his family tree is "the man who saved my father when he was a boy." That was the even that lead his father to be obsessed with Drosselmeyer--he started much of Autor's research, and trained him to become a Story-Spinner. (If you combine this with the theory above that Autor is an actual descendant of Drosselmeyer, it's possible Autor's father purposefully married into the family if he wasn't one himself.) Much of the (really weird) ideas Autor has about what one needs to be a Story Spinner were actually taught to him as a child--which would mean that, yes, Autor's father made him stand in the middle of his study for three days without sleep or food. (Which also explains why Autor is rather...interesting.)

The Princess Tutu manga is a Fix Fic written by Autor.
This explains a lot of the changes to the story in the manga:
 * Autor thought the anthropomorphic animals were silly, so he got rid of them, except for Mr. Cat because he knew too many people would complain.
 * The Ho Yay between Fakir and Mytho disappeared because he's a guy and it didn't appeal to him. All of the nudity fanservice involving the girls, and the Les Yay between Rue and a girl that looks suspiciously like him, however...
 * Edel is the evil, slutty villain in the manga because only someone who's evil would betray Drosselmeyer...plus, more fanservice!
 * The ending is more strongly Mytho/Ahiru because that frees up Rue to end up with him.
 * Fakir isn't actually Drosselmeyer's descendant in the manga. He's a nobody in the manga. This is Autor being bitter.
 * Ahiru is only a duck for one chapter because "a mere duck couldn't possibly end Drosselmeyer's story!"

However, it's unlikely that he'd try to "fix" it by leaving out himself, Drosselmeyer and story-spinning altogether.

The Story is actually part of The Tradition.
With The Tradition, individuals are forced down paths already chosen for them until they a) accomplish their "happily ever after", b) die, or c) have something else happen that allows them to break from it.
 * Even the protagonists find that completely breaking with The Tradition is extremely difficult, and can open the door for other problems if done so incorrectly. (Remember Fakir's difficulties in transitioning from the role of the Knight to the role of the Author.)
 * It also has more than its fair share of tragedy (Fair Rosalinda and Ladderlocks, anyone?), which would fit Drosselmeyer to a T.

Not sure how, but they can be guessed at.
 * Guesses, in order of speech: Disgust or anger, disappointment, hopelessness, resignation, and courage. Courage was also the one who spoke to Tutu about returning the final shard.

Drosselmeyer is into Lolicon
I don't think I have to explain myself.
 * He does show more interest in Ahiru and Rue than in Mytho and Fakir... More interest like watching in their rooms at night and giving them Stripperific outfits... I think I need Brain Bleach.

The narrator that speaks at the beginning of each episode is the REAL author of the story.
It sort of makes sense. In the last episode, Drosselmeyer himself ponders if he's in someone else's story since his didn't go the way he wanted.

Drosselmeyer, Fakir or one of their descendants created the Death Notes and maybe the shinigami too
Writing = reality, and one of them was playing around with their powers too much. The rules at the beginning of the death note, while supposedly written by Ryuk, could just be the writer who made them writing the story about the death note itself. Also, Fakir can make writing look dramatic while Light... eh.
 * Not to mention, if you take out the "F" in Fakir's name, what can you rearrange the letters to say? Kira!
 * Obviously, it should be arranged "F Kira"... That is, Fakir became the "First Kira."

Every Tear Jerker Downer Ending book you've ever read is that way because Drosselmeyer got a hold of it.
It's his mission to depress us all, to the point of suicide if possible, in revenge for losing his hands. He obviously believes in Disproportionate Retribution.

Mytho is Dios.
Once his heart is restored, he is the glorious ideal of the Knight in Shining Armour. He is self-sacrificing to a near suicidal degree (even before he was emotionless ). In Rue's flashback, we seen her as a little girl while Mytho still looks the same as he does at the time of the series - it's as though he doesn't age. Once fully awakened, he is able to save the woman he loves and defeat ultimate evil. Dios is described as "That which is eternal, that which shines, the power of miracles, the power to revolutionize the world..." and is shown as having been around since a golden age. He, too, has temendous powers of swordsmanship and defends the world form evil, at a great cost to himself.

Revolutionary Girl Utena and Princess Tutu occur in the same universe
With all the similarities and f* cked up fairy tales running around, it's no wonder. The former takes place in Japan and the latter takes place in Germany.

Drosselmeyer is the predecessor of Franz Kafka.
Upon realizing his other descendant  wasn't playing along with the story, Drosselmeyer went into the life of his however-great grandson and manipulated him into continuing the line of tragic tales by striking him with clinical depression.

When Autor grew up...
...he decided to leave town to find his place now that it was finally physically possible, somewhere along the way his mental instability increased before finally, er, "stabilizing" at its own odd point in its own odd way, his obsession with the all-powerful Drosselmeyer ended up as some kind of segue, his paranoias led to him using an alias for whatever reason, and he ended up as a cultist priest in the town of Silent Hill. ...After the English dub, at least. I swear, the voices (and, when said voices are attributed to them, mannerisms) are uncanny.

Lilie is Kinkan Town's Kafuka Fuura.
The reason she loves suffering so much is because she can't understand it; when something bad happened to her, she brushed off the circumstances as being too unrealistic, and now just enjoys the sensation so she can coddle her friends. Also, she's got a huge amount of physical strength and doesn't notice when she hurts Ahiru.

Drosselmeyer is Joss Whedon.
The first syllable of his name sounds like "Joss", and he loves angsty stories.

Mytho held on to one emotion to keep himself alive.
Knowing he couldn't live without a heart, he figured he could at least manage to survive with a small piece of it. Which emotion was it, you ask? His desire to protect the innocent. This explains why he would go out of his way and risk his life to save the lives of others, no matter how insignificant.
 * Of course, to him, no life is insignificant.

The entire series is a tabletop RPG game successfully derailed.
The PCs are Ahiru, Fakir, Mytho, Rue, and Autor. Ahiru and Fakir's players were upset because they realized their characters were doomed to die no matter what, and Autor was upset because his character barely had any inclusion in the game. Story Spinning is a power granted through some obscure splatbook that the GM approved without looking through, and they used it to the fullest extent to derail the game. The Bookkeepers are DM fiat in physical form. Drosselmeyer was a cool framing device the GM thought up.
 * Someone needs to write this fanfic.
 * The system is Changeling: The Lost. Fakir is a Darkling Archivist who took up Talecrafting near the campaign's end. Duck is a Windwing Best built a social character. Mytho is a Fairest Dancer who's cursed with low Clarity. Rue is a Flowering Fairest, manipulating all those around her. Drosselmyer is a True Fae who plays with the world on his whims.

The second season had its screenwriters replaced with Ahiru/Fakir shippers.
This troper thinks that the sole reason for why Mytho turned evil was for the sake of pairing Ahiru and Fakir together without any intervention. The Abridged Series agrees. A recent episode has Drosselmeyer complaining because the "Shipping Bridge" has focused the plot on Evil!Mythro and not the Heart Shards. Duck notices that after she made the wish on the bridge, Fakir was a lot nicer but doesn't think much more of it.
 * But nearly all of that was hinted at early in the first season (and Mytho turning evil was set-up in the first) and there was only one new script writer in the second season who only wrote four episodes (Freya's episode, Hermia's episode, the episode where Autor was introduced and the "Danse Macabre" episode). Only one has significant development for Fakir/Ahiru (Hermia's episode features the love letter subplot), and the only other one that seems to fit this theory is . Plus, all of the script writers and storyboarders from the first season were still with the show in the second season, and the creator, Ikuko Itoh, worked with the series the entire way through. The final nail in the coffin for this is the fact that the trailer for this series used to option the series for TV channels before any episodes were made features Fakir stealing a kiss from Ahiru and is shippier than anything we see for them in-series.

The transformation into Princess Tutu includes an age up.
Princess Tutu is taller than Ahiru, has longer face, smaller eyes (large eyes being indicative of youth) and has a bigger chest than Ahiru. Additionally her increased grace and poise might be in part due to growing up out of an awkward phase.
 * It's a 'duck-to-swan' metaphor, so that's probably true.
 * It's also genre-appropriate.

The Raven is responsible for Alfred Hitchcock's The Birds.
Either he escaped Kinkan or is somehow influencing the otherwise normal birds to attack humans.

Drosselmeyer was taught Story-Spinning by Featherine Augustus Aurora
And ended up like Bernkastel. Unfortunately.

Mr. Cat is related to The Royal Family
The King Cat in The Cat Returns keeps trying to get Haru to marry either the Prince or (at the end) him. However, a third option is taken. Somewhere down (up?) the line, Mr. Cat was born and ended up in Kinkan town where things got... Screwy.

Dark Voice is The Raven.
Let's see... "Black... thing with red eyes?

Captures a good guy lady and Mind Rape and invokes a Painful Transformation to turn the lady into an evil evil evil puppet?

Uses mindless drones. This one differs a little since the soul-raped victims are pretty much used exclusively by The Raven (crows) while the Dark Voice's Zerg can make some (Infected ____) but don't have to.

Drones tend to Zerg Rush."

Fakir is part Arab.
If his name and physical features compared to the rest of the cast is anything to go by.

The reason Rue doesn't become a crow despite having been exposed to raven's blood for so long...
...is because she isn't fully part of the story. The characters of The Prince and the Raven that were mentioned were the prince, a knight, and Princess Tutu. Duck took on Princess Tutu's role, Fakir was the knight, and the prince was... Well, himself. But it never mentioned any kind of crow princess. Even when she became a character, she was still separate from the original story, and that's why the power of the Raven, the villain of the original story, didn't affect her as strongly as it did. In her veins, there was the most literal mixing of fiction and reality possible, and her "real" form was strong enough to resist the outside influence. As for why  affects the townspeople so quickly, well, my only thought so far is that the story did spread to the town, and since they weren't major characters, there was nothing to protect them at that point. Still, just a thought.
 * Autor mentioned townspeople turning into crows happened in the story, so it fits that it happens to the actual townspeople.