Superjail/WMG

The Warden is The Cat in The Hat
Or rather, a reincarnation of him. Just listen to the voice.

This would make Jared a reincarnation of the fish. Note their similar purposes. Jared is there to try and keep the Warden from going overboard but always fails. The Twins would be Thing One and Thing Two and maybe Alice and Jailbot are Sally and her brother seeing as they are both guards and

Superjail is hell, and the Warden is the Devil.
Well, let's see: As for the Warden being the Devil:
 * It contains and punishes evil people.
 * The punishment is done in the most horrific way possible.
 * The path to the jail seems to be outside the normal boundaries of reality.
 * Jailbot carries Jackknife through the surreal opening scene, which is a reference to life, into the white light of death, and ends up in Superjail.
 * The jail seems to have an infinite interior.
 * It froze over at one point.
 * It's inside a volcano, even!
 * Two volcanoes. One volcano somehow formed inside of the other. Still hot, though.
 * He's extremely sadistic and melodramatic.
 * He takes great pleasure in the pain and suffering of others.
 * He's able to warp reality at a whim
 * He strongly disagrees with traditional views of justice
 * He wears purple, which is usually associated with pride - the thing that got the Devil cast out in the first place.
 * Hell, forget the purple, he is proud. He refuses to ever admit he did anything wrong, and thinks he's completely in control of everything.
 * Is a Man of Wealth and Taste, albeit a very colorful one.
 * Jared, his main whipping boy, is a man who gives into temptation almost every other episode.
 * The Twins are fallen angels.
 * Alternatively the twins are just plain angels. They make constant efforts to thwart the Warden's plans and although their methods are violent and chaotic there is something very old testament about angels smiting the legions of hell.
 * Superjail eventually turns into a Utopia once his influence is removed.
 * And here's the kicker:

Superjail controls the passage of time within itself.
Superjail loves the Warden, so it keeps the Warden young. When he leaves,, it speeds hundreds, if not thousands, of years into the future. Jared's aging in the real world would suggest that the Warden was gone for maybe ten or fifteen years, but inside Superjail,  which would have taken an extensive period of time. To Superjail, it seemed like the Warden was gone for a million years--so he was.

Superjail! takes place in the same universe as the Hitchhiker's Guide.
You KNOW it makes sense, I shouldn't need to explain this one.
 * Which same universe as the Hitchhiker's Guide?
 * Either one. Or all of them. It doesn't really matter, given Superjail's pansdimensional physics.

Superjail! takes place in the universe of Firefly.
Because it has to be said too.

Superjail! takes place in the same universe as Dead Leaves.
Dead Leaves is essentially Superjail, except in The Future rather than Twenty Minutes Into the Future. It almost goes without saying.
 * Well, a lunar base version of Superjail was part of the original pilot (in the extra features, under "An Abandoned Sequence").
 * The similarities between the two is almost uncanny. You have Warden and Galactica, who's father were both wardens, and both died in a freak accident. They both have artificial lifeforms that see them as their parent, though hardly ever act on that desire. Massacres happen once an episode (though Dead Leaves was an OVA...). They both have insane animation, and are very colorful. this almost one of those 'Chicken or the egg' type questions.

Superjail! is in the center of the omiverse, and every universe leads to it
See the last three WMGs

Superjail is a jail in an alternate universe made to hold criminals from many different universes
This is an expansion to the above. Seeing how many fatalities there are per episode (and assuming that this stuff happens regularly) Superjail would have to have an impossibly large number of inmates at all times. This can only be possible if Superjail has criminals from other universes.

Superjail, as a jail, is really a front for the Warden's plans for world domination.

 * He has numerous superweapons built without any explanation to Jared. (And why should he explain to stick-in-the-mud Jared?)
 * Jailbot is sent out to search and capture the most depraved and violent of criminals to be enclosed within Superjail.
 * He allows said inmates to kill each other with little repercussions, sometimes even promoting it, to ensure that only the strongest survive for future super soldiers.
 * Jared, short spineless Yes-Man he may be, has been shown to be a fairly competent sniper - a pretty good thing to have under your thumb.
 * Don't forget the entire plot for the two-parter season finale.

The warden is Willy Wonka.
Gene Wilder-Willy Wonka decides that the time-and-space-warping effects of his candy factory would be perfect in holding prisoners. So he decides to expend his energy in expanding the place. Took about ten years. Used outside help in establishing it. We all know Willy was a little insane...who knows what ten years might do? And Jared is an Oompa Loompa with a skin diseases. And Jailbot is simply the Great Glass Elevator (both can go anywhere) with an A.I. shell. The twins are two of the kids who had been left behind in one of the disastrous tours.
 * This troper wishes that people would stop comparing him to Willy Wonka. Totally different character! Can we just declare a total radio silence on the Willy Wonka franchise in this fandom? Please?
 * Yeah, this Troper doesn't know where people are pulling that one from...
 * Will you accept Willy Wonka's Evil Twin, then?
 * If you don't like it, don't read it.
 * Word of God has stated that Gene Wilder's Wonka was a large influence in the creation of the Warden. Personally, I'd mark the Warden as just a teensy bit too sadistic and downright crude to be Willy Wonka himself, despite the similar antics. The Evil Twin theory, though, is viable...

the Warden is from another planet/plane of existence where females do not exist.
Think about it. The first thing he says after Ultraprison crashes into Superjail is "Jared are these what you call immigrants?". In the Mr. Grumpy-pants episode he reacts to Cancer with: "What the hell is that?!" and calls her grotesque. Further proof is his ability to sorta give birth to his inner child in the same episode. Maybe his people reproduce asexually?
 * M Preg. Jared will bear his child.
 * This Trope thinks Warden has a sparkly, rainbow vagina.
 * That would explain his infatuation with Alice.

Superjail is an even more bizarre version of Wonderland.
Think about it...


 * Jacknife first gets sent to Superjail for stealing a rabbit (chasing the white rabbit).
 * To get into Superjail you have to go through a hole in the clouds (the rabbits hole).
 * Superjail, like Wonderland, seems to exist in a dimension where you can only gets there by rather strange means.
 * There's Alice.
 * The Warden would be an even more insane and sadistic version of the Mad Hatter.
 * To be specific, he's a horrifying hybrid of the Johnny Depp and American McGee's Alice versions of the character.
 * The Twins are Tweedledum and Tweedledee.
 * In the pilot episode, Jacknife is put into a perfectly normal cell lacking any of the insanity of Superjail, until he swallows the "drink me".
 * Holy crap! This makes the most sense out of anything on this page.

The Warden is Edd from Ed, Edd n Eddy.

 * They're talking about Double D. Both the warden and Double D have black hair and gaps in their teeth, and their both pretty pale and scrawny. Imagine that something makes Double D go absolutely insane, maybe Ed and Eddy get killed in front of him by a child molester, and he decides to put all of his genius towards creating a prison that can hold criminals better than the regular sort. Using his notes from the episode where his friends and himself found out the world used cartoon physics, and his wacky inventions, he creates Superjail. Jared and Alice have no relation to Ed, Edd n Eddy while Jailbot is really a pimped-out Plank, and one of Double D's first creations that was specifically for Superjail. His outfit is Jimmy's design.
 * Jossed. Word of God for Ed, Edd n Eddy has stated Double D is blonde under his hat.
 * Two words: Hair Dye
 * The above Jossing is also Jossed. That Word of God is actually a Flip-Flop of God, as the answer changes whenever he gets asked.

Superjail has only one true inmate: The warden

 * Think about it: The Warden is a classic Mad Scientist sociopath type, who we've already seen has an eye for world domination. What if TPTB (maybe the Time Police) finally decided that the only way to hold him would be to kill two birds with one stone--keeping him busy by giving him a little place of his own to to wreak havoc, and letting him use the worst of the worst hardened criminal scum as his own test subjects. This also explains the twins--they're the true jailers, and interfere with The Warden's plans to keep him in line/for their own amusement. Also, this might explain why the prison is in two volcanoes--one for the Superjail, one for the area containing the Superjail.

Going with the above, Superjail takes place in Ravenloft

 * The Warden is Superjail's Darklord.

When the series finale comes around, Jacknife will not escape.

 * He'll die unceremoniously around the end of the episode, if Jailbot doesn't up and kill him at the start or something.
 * Although, with how much the show likes to screw with people, it'd be just as likely that it ends with Jacknife being the first and only person to survive his sentence in Superjail and be set free.... Until he commits a crime about 12 seconds later and gets sent back.

The series finale will take place around the funeral of Jacknife.

 * Given how little attention is paid to the countless deaths in Superjail it would be a huge narrative inversion to end with the whole of Superjail reminiscing on the death of an inmate. What's more it would bookend the series as it the pilot opens with Jacknife's first arrival in Superjail.

The Warden being more of a jerk to Jared in the later episodes of season 1 is the result of being frozen in "Cold-Blooded"
Somehow his brain got slightly damaged when frozen and the time he thawed (presumebly by the Twins so they'd have something to do), he became more of a Jerkass because that was his attitude towards Jared in that ep and remained constant. It would explain why the Warden Took a Level In Jerkass (along with Alice and Jailbot) in "Terrordome" when in comparison to "Combaticus" they worked somewhat happily together.

Superjail takes place on Adventure Time Earth
They both have similar animation styles and similar metaphysical weirdness.

At some point, the Warden will lose control and Superjail will go critical, causing the Apocalypse that takes place in Ooo's past. The giant chunk in the Earth is were Superjail was located when it exploded.

There is more than one Superjail, and more than one Ultraprison.
In the "Ladies' Night" episode, the Warden mentions that Superjail is the largest prison "This side of Dimension 5612", a comment the Mistress dismisses as "cute". As guessed above, Superjail really does process inmates from multiple realities, and, as also guessed above, is itself its own reality, made specifically to house these dangerous criminals. In the trailer, there's even a single shot of a non-human inmate, perhaps processed in from one of these other realities. With the infinite multiverse to supply prisoners, this also allows for the routine mass die-offs of inmates.

The Warden is a Timelord
I don't know HOW this hasn't been said yet.