Tower Prep/WMG

TITANS Tower Prep
Well, it is written by Mr. Dini
 * What does this mean? What wild mass guess are you making here? Is this about the Teen Titans cartoon that Paul Dini had nothing to do with?
 * I know Dini had nothing to do with it, I'm trying to say that maybe they're superheroes in training. But not on a superman level, more like.. Batman with a useful, yet not crazy powerful ability.. So, being prepared to be a team of superheroes i'd suppose..

They're on another planet
Come on, the stars are totally different, it's pretty obvious. Plus the Nurse mentioned something about the students having no resistance to the germs there. Admittedly that happens here on Earth too but it still strengthens the possibility.

The "Gnomes" are students who tried to run. They got caught and fitted with mind-control gear to serve as mindless security drones.
No one knows what they are. No one who's encountered them has learned what they are and returned. It just seems obvious.
 * No... They're robots. Hence the mask on the flagpole and the electricity. Student who are caught are probable killed or sent to West Campus.
 * Humans can wear masks, too. Plus you haven't successfully ruled out cyborgs.
 * Ian rips it's head off and doesn't care.
 * What if the gnomes are the students sent to West Campus? They're brainwashed and possibly borged and/or genetically altered into Gnomes.
 * After what happened to Cal in "Field Trip", this looks to have been confirmed.

Whisper119 is scared too
As the only real involved character not part of the group, it's a decent enough guess.
 * And confirmed.

The Gnomes are Sleestaks
They look an awful lot like them.

The escape attempt was part of a Xanatos Gambit on the part of one of the four to demoralize the other three, particularly Ian.
It seems more than a bit convenient that they would try to escape on Ian's first day. Also Ian's roommates obviously went on an escape attempt before, since they knew about the cliffs.

The escape attempt was part of a Xanatos Gambit on the part of Senor Guapo to demoralize the four of them.
That's why Gabe clings to him so, Senor Guapo is hypersuading him to do things.
 * As seen in Dreams, Senor Guapo has talked to Gabe before, and it led to him having a parole officer.

They're all robots.
"Who are you?" is practically Arc Words. Throughout the first episode people repeatedly tell Ian "You don't know who you are," "The question is, who are you?" and the like. Not to mention the mysterious argument that Suki's electronics expert parents were having before she left, CJ's memory problems, and that static that knocked them all out.
 * And as of episode 3, we have the revelation of the hidden Artificial Intelligence lab underneath the school.
 * In the election episode, we do see a close up on their blood, and it looks like human blood. So they could be really good, human-looking robots.

Ian will join the Buffer team.
If you're trying to escape, it makes perfect sense to join the one group in the whole school that apparently has access to the outside world.
 * Just happened in episode 4.

They school is under a dome.
The sky is a projection which would explain why the stars are different, they are being broad cased are the night sky from another planet
 * Jossed.

Their parents don't know where their kids are
The only word we have that the parents know the kids are at Tower Prep is from the headmaster. He's just lying to the students to make them more accepting of their situation and not to make trouble.
 * Jossed.

Coach is a time travelling Ian from the future.
He sure seemed like a stealth mentor there.

Escaping is what they're being trained for
Until they can use their various abilities to escape, they won't be allowed to leave.
 * Part of that is right.

CJ is Whisper Version 3
Think about it... CJ has no memories before Tower Prep... Whisper 119 is scared, what is she scared of? Getting replace by CJ.
 * Half right. It was a fear of getting replaced, but not by CJ.

The Gnomes are aliens
Going off an above guess of the school being on another planet, the Gnomes are actually local inhabitants who're being paid by the school to be a security force.And given the promo for episode 4, it's possible that Coach History is their boss.
 * Debunked...
 * And don't you know to Never Trust a Trailer?

Government Experiments
All the Students are the result of experiments with mutagens and their parents were volunteers or scientists working on the project.

Alien Hybrids
All the students are alien hybrids of the species native to the world they now find themselves on. Their latent powers are to be awakened, either to guide the Earth or prep it for takeover.
 * possibly debunked

The Gang's Parents Were Test Subjects
They were volunteer for study for the Corvus tests...and (see below).

Head Master is Corvus
He started Tower Prep to keep an studying his subjects.
 * Zig-zagged. The essence of the WMG is wrong, but it's not as simple as that...

Gnome is one of the work study jobs
That's why they're students.

CJ is a mole.
When you have a story where one of the main questions is "Who can you trust?", there has to be an inevitable betrayal from someone close to the hero. How can your Evil Mastermind insert someone into the hero's team that can betray him when he's got someone who's a human lie detector? Easy - turn the lie detector. Add to this her lack of memories from her home, and she's the "odd man out" with her origins. Maybe she's done this before, having inserted herself into several groups that attempted to escape and led them to their dooms...and was almost about to finish off Suki and Gabe when they accidentally ran into Ian. Rather than let her cover drop, she's now working with them.
 * Confirmed, in a way.
 * Confirmed.

Tower Prep created the monsters in the graveyard as an early experiment.
CJ said that you wouldn't bury a creature and give it a headstone unless it was your pet. All the headstones had names in Latin like genealogical classifications. Plus, the skeleton of the cyclops looked a lot like a human skeleton. Maybe Tower Prep tried to make monster species but the experiments failed? Maybe they made the monsters out of students?
 * Jossed.

The whole thing is a Secret Test of Character to see how the students handle their special abilities, which were given to them by the school.
They're deconstructing I Just Want to Be Special. Not only are they experimenting with giving people powers, they're studying the psychological effects -- seeing which students decide "I Just Want to Be Normal" and mean it, which ones turn into Smug Supers, which ones blindly accept what they're told or try to ferret out the truth or escape... The 'disease' in "Election" is simply testing their ability to depower anyone they eventually judge unfit of the role they're attempting to groom them for.
 * Confirmed,

The staff are former students who failed to live up to their potential
As in they lost their powers. We already know that at least the Headmaster, Coach and Nurse were former students, yet none have shown any signs of extraordinary ability. Furthermore Headmaster seems more than a tad bitter over past administrations and we know of at least two things, Chemica-Desin and the Rooks potion that can remove or block powers.

Ian is Cornelius Tower's grandson.
The picture is a hell of a clue, and then there's "my liege." If Cornelius, the founder, was the first "king," who would the next one be?
 * Possibly Jossed; Ian said he knows his grandparents.
 * Pfft, as if Ian can be trusted to know for sure on that account. Him claiming it actually makes it more likely for The Reveal to shatter his preconceptions.
 * Alternatively, if Cornelius' backstory about World War I is true, that would make him over 100 in the picture with Ian. He could be his great-grandfather.

Headmaster really WAS the Great Unknown
That wasn't part of Gabe's dream, but a pause between two dreams that he concluded to be part of a dream.

The Great Unknown is the Headmaster's son.
Gabe knows subconsciously, and that's why he appeared as the Headmaster in the dream.

They're in the Bermuda Triangle.
Everything that goes there disappears and radars and compasses go haywire when near it. It would make for the perfect hiding spot.

Headmaster's plan for Ian is that he's going to be the next Headmaster if he doesn't escape.
Even what seems to be the Board of Directors is in on it. Also, Coach used to be a student; The same thing could happen with Headmasters.

They're being trained to be super spies.
It's pretty obvious. Students with more physical,"flashy" abilities like Ian's preflex, Ray's super strength and as of the latest episode  are trained to be field agents. While students with more subtle abilities, like CJ's perception and Cal's enhanced hearing are trained to be recon scouts.

The mysterious man is the 7th
The mysterious man said that  What if he knew that there is a plan that Ian is a part of?

Tower Prep is a Super Breeding Program
The goal being to force people with complementary powers to hook up. Ian and CJ, preflex with great attention to detail would be a closer-quarters combat powerhouse. Suki+Gabe, ability to change your voice to mimic anyone, and the ability to compel people to do what you want. Every generation coming closer to real supers.
 * What about Ray's strength or that super fast kid from episode 2? What powers could their parents have had to make them? In fact,a lot of the kids' powers seem like they must come from interesting combinations. Ian's preflex is basically precognition + enhanced reflexes = Spider Sense. Ray must have inherited enhanced endurance and something else to get super strong.