Megatokyo/WMG

Dom is a sysadmin
He uses "fsck" as an expletive. If you need to use fsck(8)...well, you aren't having a good day, to say the least.
 * It could just mean that he is a hacker. Largo also uses fsck as a swear.

The Cave of Evil is a Freehold. Most of the regulars are some sort of Changeling.
The Cave of Evil is all about manipulating emotions, particularly that of "the horde", all those otaku/zombies that infest the place. The folks that run the place use it to soak up all the emotions that they generate and thus replenish their glamour. Tohya, the queen of whatever court it is (I'm not really sure), is some form of Fairest who has found herself in over her head with manipulating people, and is worried that all the commotion will draw the attention of the True Fae. The main cast is occasionally allowed to pierce the Mask, but only Erika and Largo have any real idea what's going on, and Largo is tempered by his general bug-fuck craziness. Komugiko is obviously Beast Seeming.

The Megatokyo Forums
Virtually everything ever theorized upon or suggested in the Story Discussion forums. Period.

Meimi is actually Kaitou Saint Tail and Yuki will soon take her place
Think about it: Meimi is St. Tail's civilian name, Yuki is an Impossible Thief kleptomaniac and St. Tail is a Kaitou, Yuki's ponytail looks like St. Tail's but black, Meimi's cross, the sheer number of Shout Outs...
 * This is all but canon. They have gotten as far as her code name starting with Mysterio... As in, Mysterious Thief Saint Tail.

Ping thinks Largo is Piro's Gay Option.
Because it's funny. And because when you hang around five girls and one guy, most of whom are attracted to you, there's only so many ways someone like Ping can take it.

Junko's dad might be the Nintendo Representative ala Dom (Sega) and Ed (Sony).
If this troper remembers correctly, Dom and Ed were talking about how they chased off the nintendo Rep a long time ago in some of the earlier comics, and just recently we saw Junko's dad pointing a Wii-mote at Ed, shouting "STAY AWAY, YOU BASTARD!"

Compound this with the fact that he deals with raging alcoholism (possibly due to the loss of his job) AND he somehow knows who Ed is and what his intentions are. Despite never meeting either him or Dom before.
 * Considering that he has been seen waving a Wiimote threateningly recently, this guess may have some substance behind it.
 * That and his screen name is apparently "Marios_Paw".
 * Of course, in Ed's case, it's kinda hard to mistake the intention of someone dual-wielding shotguns.
 * Specifically, in the earlier comic in question, Dom mentioned a Nintendo representative that he and Ed "chunked" when Sega was promoting the Dreamcast and about how Nintendo hadn't been able to find anyone to replace him. Flash forward about 400 strips to Junko's father mentioning "that position I haven't been able to fill... for years". Add in Junko's father's rather disparaging words about Ping (a Sony product) and the fact that he's scouting Miho like Dom has been scouting Erika and Kimiko, and, well...
 * also, the things he says about Ping basically amounts to "interfaces should bring people together, not separate them." Nintendo's latest system, the Wii, is all about personal interaction while games on Sony and Microsoft systems have the potential to alienate people (take a shot whenever somone insults you in Modern Warfare 2 online. Soon you won't be able to hear them properly).
 * And now, in his latest appearance, he has seem using two Wiimotes as weapons (to summon a huge L block).

The Cool Thing will end up doing something important eventually.
It just has to. Because it'd be epic.
 * Such as the possibility of Yuki's pet chibi/zombified 'zilla eating it (as he/it is wont to do with pretty much any technological device) and transforming into a chibi/mecha 'zilla (my own Wild Guess, perhaps not in the Mass category, but still...).
 * I thought it controlled the ph33rb0t5?
 * The Cool Thing is currently making Largo at least half, if not fully, indestructible. Remember the power line incident?

Miho's first hospitalization was due to an attempted suicide.
Or at least, that's what she lead Piro to believe. She may of may not have been lying.

Largo is a spark.
He's unnaturally good with technology, including technology that should not work, is definitely insane, and his 1337speak is likely analogous to the sparks' jagged speech bubbles.
 * Alternatively, Largo is a (Grimm) Genius: The Transgression.
 * Grimm? I'd say his personal style fits Staunen more. Although he's more likely to be a Spark, given that he seems to have very little Jabir and his tech doesn't seem to have Havoc problems.
 * Related to the above, if/when Piro finally gives in to Largo-vision becomes Inspired, he will do so as a Klagen.
 * The zombies are manes!

Miho is some sort of 'archetype'
this strip implies that Miho is an analogue of some sort, and earlier strips mention that Miho represents a certain type of story. It is an established fact that in the Megatokyo Verse, people who can manipulate society (like Idols) are extremely powerful. Most likely, Miho represents an entirely new type of character, off which others are inspired/based/influenced. Kimiko is one most likely as well. Part of the Issue with Miho's 'Representation' is that she is also an MG, thus adding another layer of complications. However. being old pro's at this, the TPCD is equipped with these 'analogue support facilities' to provide safe, secluded locales where 'Analogues' can recuperate. Obviously, Miho's particular character type can, under rare circumstances, cause 'players' to actively undermine the system, even if they don't realize it. Obviously, all of this is expensive, so EDS systems are likely designed to replace Analogues with something more predictable and controllable.
 * There also seems to be the implication that she was a real person at one point, since Junko's father brings up how no one knows what her original story was, just how powerful, endearing, and enduring it turned out to be. Miho also hints at this while she was complaining about Kimiko's attachment to the Kotone character, and during her rant at Yuki. This changed after people stopped caring about her and more about the emotions she invoked in them. Her MG status could be either a representation of the archetype she Analogues, or she could have been one originally. And now she seems to be worried about people "reconstructing" her...

Megatokyo is a huge Alternate Reality Game.
It's in the future, where the internet is a whole lot more advanced, and takes place in a sort of 3-D Second Life realm designed specifically for ARGs, where each 'Verse (or a couple of geographically disconnected 'Verses) takes place on its own server. The "mOh in Real Life" ARG series (with Pyro as the primary focal character while other points of view happen simultaneously) takes place in the aftermath of the "Girl Phase" ARG (a much more simple game with focus on Hayasaka), which is why the Girl Phase/Moeko/Erika fans came crawling out of the woodwork once it was revealed that her character was being revived. The server also has a Fantasy Cop sim running, but Largo and Yuki are the only characters to play both games at once (Largo because he's a major part of mOh iRL and already used his avatar on that server for zombie pwnzing back in the 'States, and Yuki because her parents were married in-game, where her father was a moderator on the Fantasy Cop sim and one of the games her mother played was the Girl Phase ARG). Most people just ignore the other game, since Visual Novel ARG players not signed in to FPS/SHMUP/Tekken games on the same server are exempt from anything more than comical damage from those games. Point of evidence: This guess was inspired by the Magic Skirt page, where it was explained that the main universe characters have Magic Skirts but the "game" characters (such as in Endgames, that fighting game Largo and Class President played, and [insofar as a Magic Skirt can be detected there] the non-Quake FPS) do not. Whle I'm here, I'm Wild Mass Guessing that Grand Theft Colo and unMod are alternate server games that the players enter to unwind in their free time, and Circuity was an Omake for the mOh/Girl Phase combined story (not unlike the more serious one that the .hack universe had) released as two special events.

Largo is an alternate-universe Kamina.
Obviously. Why hasn't this been posted yet?

At the end Piro and Largo will choose to stay (as in I Choose to Stay) in Tokyo

 * Think about it. In Tokyo they have girlfriends, a job and probably better living options that they have home. If they ever return to the states would be more to pick up their stuff there to move back and to be able to adjust their legal situation.
 * Adding to that, I've thought in the past that perhaps Piro might choose to stay while Largo returns to America with Erika. The reasoning has to do with a few things. First, Erika can speak English while Largo can't speak Japanese, so if they get together permanently it could be easier for him to function in an English speaking society without any language disadvantages for Erika. Erika probably doesn't have as much focus in America as she does in Japan as well, which would make it easier for her to live a less stressful life. Piro would choose to stay in Japan with Kimiko as she, like Largo, is monolingual and doesn't speak English. He also seems to be much more at home in Japan than he seems to have ever been in America anyway.
 * Alternatively, Largo and Erika stay so that Largo can be head of TPCD, showing them how to really handle disasters and monsters.

Fred hates Megatokyo.
He admitted the reason he even drew the first couple of strips was so he could shut Rodney up and stated that if Penny Arcade never linked them, he wouldn't have done any more. Over the years there have been lots of filler, hiatuses and half-finished strips. There was a point in 2009 where he was weeks behind his update schedule and without even uploading a filler page, he took a vacation for two weeks. And this is his full time job, so he relies on it to support his family, as does his wife since her job is the business side, so you'd think he'd be more focused on it. I think he just does it to sell the merchandise and for the fans he's acquired.
 * Does an astonishingly good job of it, if true. His commentary in the print volumes heavily suggests otherwise, though.

Ed's gonna need some more facial reconstruction surgery.
At the end of chapter 10, the Cave of Evil goes boom with him at the epicenter. and given his tract record with this, it probably is going to happen again.

Largo is Calvin grown up.
'Largo' is clearly a pseudonym. The personality and detatchment from our reality match.
 * But why would he need Boo as a conscience? He had/has Hobbes.

Penny Arcade, PVP, and Megatokyo are all part of the same universe
Basically, the idea is that all three webcomics are really part of a single universe where there is No Fourth Wall and the authors of each of the strips are Physical Gods within the universe (except Piro and Largo are unaware of this for some reason).

For more information, see the relevant theorem at the Penny Arcade WMG page.

Ed is Largo's Evil Counterpart.
Gonna feel really stupid if Fred's already said this, or it's common consideration, but still.

Of all the characters in the strip, Largo shares the most in common with Ed (Dom is close, but a little too intelligent and favoring of other methods), especially in how they react to Japan. Both are hardcore FPS gamers, both have serious hard-ons for flashy, immensely destructive weaponry, both take to the mech-piloting, 'zilla-riding, zombie-blasting, robot-fighting side of (Mega)Tokyo's reality like ducks to water...and both become progressively more "insane" (relatively speaking) as a result. Largo, however, gets his madness tempered somewhat (especially by Erika, but with some significant input from Boo and Junko, as well), and he comes with his own (mildly skewed) sense of honor to begin with. Ed, on the other hand, is given carte blanche by his employers to kill Ping (with the mild caveat to stay away from Erika), given the ability to essentially respawn in RL, and his schemes to carry that mission out get increasingly violent; everything in Ping or Miho's general area has become, in his words, "entertaining collateral damage." There's also hints (well...strong hints) that he was something of a psycho to begin with.

By this point, Largo has managed to reconcile his reality with some semblance of normality. Ed, on the other hand, has submerged in that reality, and with his recent failure to permanently kill Miho, he's finally become totally unhinged.

Largo's view of reality is the correct one while Piro lives in a delusion
Basically all the zombies, zilla's and Ninjas exists objectively while Piro lives in Dating-sim fueled delusion.

Fred hinted at this in his rant, basically saying that we readers just assume that what Piro sees is true because its more mundane. He then says that there's something odd about Piro's world. It will be and interesting twist.
 * This is assuming that one has to be a delusion for the other to be fully real. If Piro's world isn't real, there'd be no "Kimiko protection organization". If Largo's isn't real, Masamichi is clinically insane.

Emotional Dolls are based upon R.O.B. 2.0
Because the pattern for Sony products is that they tend to not be as innovative as other lines, but the systems have better specs. One could imagine that, in a world with as loose physics as Megatokyo, they could improve Rob to sentience. After it was released, Sony made it look realistically human (Rob would probably still look like he did before, but bigger).

Piro ends up with Miho in an unexpected First Girl Wins
The recent comics seem to be going in this direction with Piro and Kimiko's implied relationship problems and Piro's path of reconciliation with Miho. In the current chapter Piro has also let Miho stay in the apartment, at least for the moment so they can talk things out when he can get some time to speak with her. As she can't go back to her house or the hospital now, it's conceivable that she might end up staying with them for while (which, on a side note, would stir up a lot of drama because of Largo's reaction that would be simultaneously hilarious and awkward to watch) which could also help them get closer. There are definite trust issues, but Miho quite possibly (still) has feelings for Piro and she's also quite good at getting Piro to open up and talk about things, however resentful he might be. Honestly, I hope it doesn't happen; I enjoy watching Piro and Kimiko's relationship change over time as it matures and look forward to it working out in the end, but it's certainly plausible that he could end up with Miho instead. Of course, all that assumes that Miho, implied to be some sot of game archetype with sad overtones is even capable of having a "good ending".

Mega Tokyo is a mass interaction of gamers playing different games and only Miho, Largo and Piro are 'real'
The Zombies are real zombies and so are the Zillas - in a game. Ed & Dom are NPCs in something like Grand Theft Auto, Ping, Erika, Kimoko and the rest of the girls are NPCs in dating sims. It explains why they just happen to work with (and date) not one but two popular performing idols, how Largo was able to get a job teaching English and all of the other craziness in the series. It's all just games. Yes, this means Piro will end up with Miho or no one.

Largo isn't as crazy as he seems
Okay, obviously, but I meant more his speech patterns. As someone said on the main page: There ere two Largos--the one from before he found the book in the sewer, and the one after. I propose its something else: The behavior shift is completely intentional, and based on realizing who Miho was.

On several occasions, Largo has described video games as a conduit for the soul, and at one point explicitly told Miho that his training his students in gaming would keep them from falling prey to her. At the time, it just seemed like crazy talk, but with everything else we've seen (and the fact that Largo has proven to be pretty much immune to Miho), its quite likely its true.

Conclusion: l33t speaking, loud, crazy Largo isn't Flanderization or even Characterization Marches On--it's his battle mode. Once he concludes Miho is no longer a threat, he'll settle down a bit.

Despite what Fred said, everything we see is real
Recently, the author suggested that large portions of the comic, including the entirety of Kimiko, were just figments of Piro's imagination. I say he was just being a Teasing Creator. Why? Because we've seen multiple scenes from only Kimiko's view, people who have nothing to do with Piro interact with her, and the story makes zero sense if you just cut her out wholesale. Would it be a twist? Sure. But it would be bad story writing, and a cruel trick on the readers.
 * Agreed wholeheartedly. I don't think anyone is delusional. They just live in an extremely complicated/messed up world.

Most of Tokyo is actually made up of androids
Think about it. The police only seem worried about the deaths and emotional well-being of named characters, and yet they organize "events" that cause hundreds of causalities. Also note here, where a zombie notes that "This Tokyo. No one's brain real." So, basically, What Measure Is a Non-Human? is well in play here--the police are sacrificing countless robots so that the various enemies of Tokyo don't kill actual humans.

This also explains the zombies' actions a bit better. It's clear that the androids are advanced enough to be infected, so they were planning on using the "event" as a stepping stone to actually conquer Tokyo.
 * Do we ever see casualties? We see buildings destroyed, but since these events are planned, they could be evacuated beforehand. Then there's all of the Magical Girls and Ninjas running about, protecting civilians. There may in fact be no casualties; there's no way Tokyo could posibly function with such a high death toll.

Miho is Lain.
Or  This is based completely around her hairstyle, but think about it.

Yuki is the "next Miho"
Yuki's life is taking a turn for the worse. She's already physically wounded Yutaka once (by falling on him), and considers herself a "monster" after dragging Miho half-naked to the COE. In 1326, Yutaka seems to be seriously wounded again. This could result in him dumping Yuki to save himself from further injury. Yuki will not take this rejection well, as she'll know that it was due to her hurting him. That rejection, and the fact that her main "skills" are teleportation and theft, could drive her to become a "Dark Magical Girl." This could effectively turn her into a Miho-like "character."

Think about it: Miho seems to be defined by some "tragic story," and tends to fear relationships (if Piro's account of their relationship is accurate). Could not Yuki be in the beginnings of her own "tragic story?" Now that many people have found out about the "real her," Miho may be forced to end her "tragic character" persona. Reaching closure with Piro could also have the same effect. With Miho thus "retiring," Yuki could take her "character's" place.

Kimiko and Piro's daughter will be names Kotone
They are already the Official Couple, and when (/if? Yeah right) Piro gets hired as an artist for the project, they will be working together to "create" Kotone. Add and If You Know What I Mean and you're halfway there. Once they settle down for real they will have a daughter, and name her after the character.