Johnny the Homicidal Maniac/WMG

Nailbunny was Fillerbunny before he died.
One thing we know is that Johnny bought Nailbunny from a pet store and fed him once before nailing him to the wall, so this is how I see it going: Fillerbunny somehow escaped the lab he was kept in only to be captured by some people in a pet store. Filler probably constantly begged to be killed and this was enough to drive most people away from buying him. So along comes Johnny, who maybe felt sorry for Filler or thought his agonized screams for mercy were amusing or just thought a talking rabbit was kinda neat, and so he bought him. After feeding the rabbit only once, he got tired of the constant noise of "They're going to find me! They're going to come get me back, they always do! Please JUST END IT BEFORE THEY FIND ME!" and so Nny finally complied. Unless he bought him for the express purpose of putting him out of his misery, in which case that one feeding may have been a sort of last meal.

The C. stands for Carson.
Hence the conspicuous lack of all too obvious "Heeeeere's Johnny!" jokes anywhere in the series. At the end of Squee!, Johnny seems to be able to interact with other humans and not act like a big bag of crazy, so without the influence of the lock-system, he may be able to hide his psychosis a little better. Perhaps even well enough to become a comedian and host a late night talk show (Not like he would be sleeping)? Big problem: Nny is probably somewhere in his twenties and when Mr. Carson was in his twenties, it was the forties-fifties. Concerning this apparent anachronism, I propose that because JTHM already seems to exist in some alternate, goth filled universe, their version of the forties/fifties was probably very different from our own.
 * Jossed. According to Word of God, Nny's supposed to be Hispanic.
 * Carsoñ?
 * I like the idea of Nny being Johnny Carson in an alternate universe: a Gothiverse, if you will. But I think the absence of "Heeeeeeere's Johnny!" jokes is more about Vasquez not wanting to do a joke that lazy.

Squee's father is Johnny's brother.
Think about it. They have the same last initial, and despite Squee's father being a total asshole, Johnny hasn't killed him. Now, he did say it's because a kid needs a dad, but he's killed countless fathers before, right? Exactly. What makes Squee's father different? If anything, he's more of an asshole than the average victim of Johnny.
 * No, what makes Mr. Casil different from other father figures is that Nny knows said father figure's kid personally and doesn't want to cause him any mental damage. Also, his main targets seem to be mid-twenty year olds out socialising, hardly the discription of the average parent.

The Moose is Zalgo.
C'mon, it's obvious. All that talk of him "waiting behind the wall?"

Johnny is a Marauder.
Johnny never gets caught, and his crimes defy reality because he's using magic unconsciously to escape. The massacre in issue three really started straining the fabric of reality and paradox. When he goes to hell at the end of issue five, he didn't die, he simply gets shunted into his own paradox realm.
 * There's a possibility he was an infernalist mage before he went mad. There is a specific ritual in Dark Thaumaturgy that involves painting a wall in blood to summon a demon...Maybe Johnny just continued to perform the ritual out of habit, keeping the demon bound.

Krik is black.
Am I the only one who seems to notice this? Every colored drawing of JtHM shows Krik with very pale skin, when it's all but spelled out that he isn't caucasian. Take, for example, the way he behaves and dresses. It seems highly reminiscent of a black man in the 90s motivated by gangsta rap music. He's a misogynist, he curses constantly, and he's constantly trying to accentuate his manliness to the point that he'll beat up a "fag" like Nny just for being skinny and dressing differently. Not to mention the fact that Nny stated his crime against society as thus: "Using racial oppression as a crutch while only reinforcing old stereotypes". If you read closely, it would seem that Jhonen didn't think too highly of black people during that time.
 * I would love to continue this with "Nny being hispanic shows he wasn't liking much of anybody during this time" but, alas.... I'm really sure the reason you're the only one to see it is because it doesn't exist. Eminem and Fred Durst etc where also popular during this time along with all the little white boys playing gangsta. As you mentioned, even the coloured drawings show him white. The few black characters Johnen has are typically shown dark toned. Except for your last reason, that all seemed very stereotyped against black people yourself :/
 * Most of the things I listed aside from the last one were padding, I'll admit that, but the last point I made is still important. I doubt that, in the 90s, Nny would have been ranting against a white man pulling the "race card" and using it as an excuse to act like a thuggish buffoon. Also, I don't recall Jhonen ever drawing black people in a "dark tone". An example is Tenna/Tonja, who outside of the full-color I Feel Sick series is never given any shading that would indicate a different race. Another example is one of the random people Johnny kills in Cafe Le Prick(I think he put a meat cleaver in his face) who was sporting a Fresh Price-era Will Smith-style haircut. I don't think he was dark-toned, either.

Tak and Dib are Johnny's parents.
Tak's human form looks an awful lot like Johnny already but combined with Dib it would be identical.

Also it was said his parents were killed by a bad man, by both Tak an Dib's definition wouldn't Zim be a bad man? Angered by losing his mission (or perhaps a little bit of Ho Yay ) Johnny would watch Zim kill his parents making him slowly go insane, also explaining his hatred of aliens.

Another bit is that if you look REALLY closely in I Feel Sick in Devi's apartment there is a strange looking statue thing that looks a lot like GiR... Perhaps Dib managed to steal GIR and that's what made Zim so upset and then after his parent died Johnny gave it to Devi as a gift. This also explains why there is a poster of Zim in Squee's bedroom in both alien and human form.
 * Probably not. Invader Zim seems to take place in the future of Johnny's world, not the past.

Johnny is Squee's biological father.
If what Reverend Meat implied is true (that Nny had sex with someone before his amnesia), the girl he did it with may have been Squee's mom. By the time she found out she was pregnant, she would have already been with the guy now believed to be Squee's dad. Believing the kid was his, he felt obliged to marry her and take care of him... Sort of... Half assedly at best.
 * All things considering Nny is very protective of Squee, It's almost as if he knew when he first saw him that Squee was his son, so he tried to preserve the poor kid's sanity so he didn't turn out like he did.

Johnny's mother died in child birth.
I dont remember anything in canon to disprove this, so why not? We don't have any background on Nny, except his parents were killed by a bad man, his dad could of been killed by some murderer, but what if Johnny considers himself to be a bad man, and what if he thinks he's the reason his mom died, it kind of makes sense in a way.
 * If this is true, another interesting possibility would be that, since his parents were said to be killed by a "bad man" and not "bad men", that Johnny murdered his dad.
 * That write-up was a send-up of Batman's origin, not canon.

Johnny was resurrected in a similar but parallel universe.
Instead of going through the hassle (or impossibility) of reseting the universe to a particular moment in time after billions of years existence, Johnny was sent to another universe whose history is pretty much the same as the one he was in before, aside from the fact that there was never a monster behind the wall in this one. This could explain a few things, like how both doughboys are stabbed to a wall instead of just D-Boy (or having them both still torn apart in the basement), why Jimmy reffered to the Taco Smell by a different name and how Reverend Meat seemed to have come out of nowhere.