Wayside School/WMG

The series is the American Version of Azumanga Daioh.
Seriously. The series and show features an Adult Child Cloudcuckoolander Teacher, Cows (in replace of cats) that roam the school, and the gym teacher is the Only Sane Man.
 * I like how I was thinking of that show the whole time I was reading this. You may have a point there... maybe Osaka got sent to Japan after the school closed?

Ms. Zarves is Canada.
Wait, who was I talking about, again?

The 19th Story does not exist.
"Miss Zarves teaches the class on the 19th story. There is no Miss Zarves. Understand? Good; explain it to me." Okay -- In the second book, Allison, for a while, didn't exist (for whatever reason) when she stumbled onto the 19th Story. The root cause of Miss Zarves' frustration in the third book is the fact that she and her class don't exist, and hence, nobody notices them (for obvious reasons) except The Men in Black because, well, they're Men in Black.

The 19th Story is a Matrix.
The Men in Black keep Miss Zarves and her students from leaving to maintain the conspiracy. One of them is the Builder who "forgot" to build it.

Miss Zarves is True Fae.
She imprisons children (And a cow) both real and imaginary and in her strange dimension where time is screwy. Among her students is an imaginary little brother made up by a student, an alias made by another, and a 32 year old woman who's never, ever been to a bathroom.

The cows that take over at the end of book 2 were intentionally placed.
They were covering up some governmental activity on Floor 19 over the next few weeks. This would explain how one of them ended up on Floor 19 in the third book.

The 19th story really is in Another Dimension, but does exist. The missing floor was caused by...
...the plan for there to be no 13th floor, since it is supposedly unlucky. Because this was put in sometime after the sideways construction started, they had to make some screwy adjustments once they realised they were now building a skyscraper instead of a horizontal building complex. The 13th floor was supposed to be the one that was empty, but they screwed that up too. So the result is that there is a 13th floor, but no 19th. The fact that somehow the 19th floor exists in another dimension is probably just a result of the general weirdness that surrounds the school.

The 19th story is being forced into an alternate dimension because everyone thinks it doesn't exist.
Fairly Self Explanatory.

The entire school is a Tardis
Explains the weird infrastructure, the freaky-deaky teachers, the heroic staff that combat the teachers, being able to fall out of it with little injury...
 * The temporally and dimensionally transcendent 19th floor...complete with perception filter...

The 19th story was built around the invisible Old One that caused the strange events and sideways building in the first place.
If the builders used anything remotely resembling blueprints, the rooms should have been sideways. Nobody noticed that the building was being built sideways until it was finished, and the builders didn't forget about the 19th story, the just forgot that they remembered it. It can't be Miss Zarves, although her memories of never being noticed may have been a result of the creature trying to make her completely dependent upon it. The halloween episode where the original teacher returned was all a mass hallucination. The 30th story is actually one of the least weird stories, and the stories closer to the 19th are too scary to knowingly put into a childrens' book.
 * Stories about weirder and scarier floors would be awesome!

Wayside has the largest playground ever allotted to a 28 (29) class school.
The builders were given land to build a 30-room across, 1-story building. They made a 30-story, 1-room across building. The playground must be comparatively huge.
 * This is actually canonical; I can't remember where, but one of the books specifically mention that the kids like having the school built that way for this very reason.
 * It's mentioned offhandedly in the introduction for the first book.

Louis arranged the vertical/horizontal dimension switch.
Because, as the future playground supervisor, his power would increase with the size of the playground, until the playground itself was greater than the school. (And, in the Wayside universe, nothing Does Not Work That Way.)

Wayside school was the school building designer's way of saying "I've got a giant tonker."
There was no mistake. If you think about it, the first floor (with the administrative offices and cafeteria) must be significantly larger than the 30-student classrooms. Especially if there's a gymnasium, the shape of the school is going to look a certain way.

Wayside School was desgined by Bloody Stupid Johnson.
Uh...yeah. A story that is in an alternate dimension, odd blueprints. What else would you think?
 * I concur. Only Bloody Stupid Johnson could end up building a nonexistent floor in a skyscraper that was supposed to be a single story...

Miss Zarves does exist!
Really! I returned a seating chart to her once that I found on the stairs above the eighteenth floor. The class pet is a cow. It has its own desk. That kid from the 30th story was there, ask her!
 * Yeah, I'm just going to get the nurse now...

Miss Zarves is a Time Lord.
'Nuff said.
 * And the 19th story is her TARDIS!

The 19th story is purgatory
In Wayside School is Falling Down, when Allison is on the 19th story, the only other sane one there wonders if those on the 19th story are dead. Since it can't be Heaven or Hell... "Myron: Maybe we're dead. Maybe we died and went to- Allison: This isn't Heaven! Myron: That wasn't what I was going to say. Allison: But she seems so nice. Could someone as nice as her really be the Devil?"
 * Wait, why can't it be Hell?
 * The possibility of the 19th Story being Hell was directly mentioned in the book without using the word:

Wayside School is built upon a Hellmouth
It would explain the wierdness and everything...

The 19th Story is an SCP Foundation.
Call Dr. Clef.

The 19th story is where people go when they are ignored too much
Miss Zarves explains in the third book that nobody ever noticed her growing up. Perhaps Bebe's parents really did have a son named Ray but they ignored him so much that he disappeared. Bebe still remembers him a little bit which is why she used his name in her lie. Perhaps that's why she called him her baby brother when he's clearly older than that (only a few years younger than Bebe). She remembers him being a baby. Allison ended up there after being ignored by her class but she managed to defy the system and get back. Nobody acknowledges the fact that Mark Miller is really Benjamin Nushmutt so on the 19th story it's reversed. The name that's ignored is the name that he's acknowledged as. Virginia and Nick's backgrounds are unknown but it's certainly possible that they were ignored to the point of non existence too.
 * Additionally, the 19th story was ignored too. The teacher that was supposed to teach there quit for some reason (probably having something to do with the mixed up building or general weirdness) and they had so much trouble trying to find a good replacement that they gave up. After a few months of no one acknowledging the floor as anything other than another landing in the stair way, it became a place for ignored people.

Myron will die.
In Wayside School is Falling Down, Myron chooses to be free instead of being safe. This seems to work because he doesn't have to learn ballroom dancing like the other students and they complain that he never has to do anything. So that should mean that he's not safe. Nothing has happened to him yet but it will. Plus, Myron seems like a really nice guy so maybe he is Too Good for This Sinful Earth.

Floor 19 exists, people just joke.
When Allison goes there, it was All Just A Dream because the story was built in to the wall.

Wayside School exists on a discworld
Not the Discworld mind you, a discworld (perhaps one of the young discworlds that appear at the end of The Light Fantastic). Where the main Discworld runs on Narrative Causality Wayside's discworld runs on that special brand of logic that children follow.

The 19th floor is a room in The Dark Tower
Come on. It's the 19th floor. Filled with fictional characters. Need I say any more?