The Colbert Report/WMG

Stephen is a Time Lord.
You knew it was coming, but there's serious evidence for this one. The studio moves around unpredictably (that episode where he was broadcasting from inside an airport departure lounge, anyone?) and apparently spends most of its time on top of the Statue of Liberty (look closely at the cityscape by the interview table) without anyone ever noticing it. Obviously the chameleon circuit actually works on this one. There's also the way that he can fit ridiculous amounts of stuff under his desk or into small spaces (John Oliver in a suitcase, two Starbucks(es?) in the shelves under the desk) and the way that certain parts of his backstory don't quite fit together. Either he's forgetting parts of it, making it up, or he's been around for a lot longer than he's letting on. Interestingly, this would account for the 'psychic' WMG nicely as well. He doesn't need to predict the future, he's already seen it. Then there's the alien financial advisor, the way he never doubts stories about alien life or bizarre technological advancements... And doesn't "The Pundit" sound like a great Time Lord name?
 * Clearly, the bears are not what they seem.
 * He was shot in the heart by Conan O'Brien, then sat up. The only explanation is a second heart!
 * Alternately to his TARDIS being on the top of the Statue of Liberty, his TARDIS is the top of the statue of Liberty (the arm with the torch, at least). A few years back, he crashed into the statue, breaking off its arm, and the only thing that wouldn't be noticed with the arm missing would be a replacement arm. This is why people are no longer allowed in the torch.
 * The predictions fit too... This is heavy Doc.
 * He's also Santa.
 * This one just got more worrying. Watch this clip and listen carefully to him tapping on the desk at the start.
 * Time Lords have more nerve endings in their stomach than in their brains, and Stephen doesn't know that it's not true for humans too.
 * Another thing I've noticed about Time Lords is that they tend to think very highly of themselves, they scream a lot, and they like bananas... hmm...
 * So this means the entire audience and the production staff are his companions! Wow...
 * This is getting hard to ignore. An hour ago as of this posting, Stephen posted the following on his Twitter (StephenAtHome):
 * In this interview he casually suggested that he might be from 500 years in the future.
 * When Colbert is re-recieving the SuperPac powers from Jon Stewart, it looks an awful lot like he's regenerating. Coincidence? I THINK NOT!
 * ...I think it's been confirmed.
 * ...I think it's been confirmed.

Stephen is psychic.
The DaColbert Code (five completely accurate Oscar picks using nothing more than random 'Six Degrees Of Kevin Bacon' reasoning) is just the latest example. On Election Night 2000, he predicted "unwinnable war" and a "downward spiral" for whoever was elected. And we all know how that turned out. This has worrying implications for his statements about the Rapture and the Zombie Apocalypse.
 * Although it seems he isn't entirely aware of his precognitive powers, because in a recent installment of The DaColbert Code he kept somehow predicting Barack Obama would become President even when deliberately using clues that would lead to McCain.
 * The most recent The DaColbert Code for the 2009 Oscars was also completely accurate, giving more credence to Stephen's psychic powers.
 * He was predicting people throwing shoes at President Bush as early as January 2006.

Stephen is a Reality Warper, possibly a reincarnation of Haruhi.
Alternative explanation for the above. He didn't predict those events, he caused them.

The 'real' Stephen is fake, and the 'fake' Stephen is real
The Stephen Colbert of The Colbert Report may seem to be a satire to point out the ridiculousness of the Republican Party in America, who is played by the real Stephen Colbert, a Democrat. However, the Stephen on the show is the real one, and the 'real' one is what the actual Stephen thinks is satire. This is why he has shown up at Meet the Press and the infamous White House Correspondents dinner in character.
 * Also, an attempt to run for President without any political experience is exactly what a satirical character would do - but Colbert was running as a Democrat.
 * Apparently there's been a study that shows Colbert has conservative fans who believe exactly that: he "only pretends to be joking".

The 'real' Stephen Colbert is trying to take over the world.
All of his actions are a careful plan to amass millions and millions of loyal followers. His run for president was merely a "dry-run" to see how close he was.
 * According to one interview, Colbert 'used to joke about how he "wanted to major in mass psychology and start a cult."' He wasn't kidding.

Stephen is a troper.
"Personally, folks, I think we have enough messages on TV. Like 'husbands are fat and dumb', 'wives don't want us to have any fun', and 'black woman are sassy and wise'."
 * When his kids ask how something works, and he doesn't know, he tells them that "A Wizard Did It." In those words.
 * I rest my case.
 * Confirmed!
 * "Don't worry, in movies you can always outrun the fireball."
 * "2012. The Mayans warned us. Assuming, they warned us one day that computer graphics would strip movies of any plot or characterization and turn them into mindless orgies of Destruction Porn."
 * One of his favorite ways of messing with us may be reading these theories about him and "confirming" them on his show. If this is the case, then we're in for a hell of a good time.

Stephen is being mind-controlled by Marik from Yu-Gi-Oh the Abridged Series.
He is being made to brainwash America through his television show. His fans have shown a creepy tendency to do whatever he says; if Marik makes Stephen to tell his fans to do something, they'll do it. Thus, Marik can enslave all of America. And his name is Steve.
 * No silly, Stephen IS Marik from Yu-Gi-Oh the Abridged Series.

Stephen is the Second Coming.
He's religiously conservative, has no doubt in the supernatural (wizards, demons, et cetera), preforms miracles (having infinite space under his desk, bringing styrophome cups to life), and has created a cult following for himself. He also seems quite confident that Jesus is White? How does he know? Because he is White, and he is Jesus! When he once saw his own face in a cup of coffee, it was the same phenomenon as when people see Jesus's face in pieces of toast.
 * He has stated repeatedly that he doesn't see color, and thus only assumes that he is white based on what people tell him.

Stephen is the Anti-Christ.
And doing a very effective job of distracting people from the real Second Coming, Jon Stewart.
 * Well...Jon is Jewish...

Stephen is a wizard.
This is how he is able to store all that stuff (up to and including two Starbucks) under his desk, and why he can communicate with ghosts. It's also why he doesn't doubt in the supernatural. Abraham Lincoln's skull is a magical artifact he uses in his rituals. ""I also do children's parties.""
 * Better version, he's the wizard. The one who did it. That's right, he's Sarda.
 * Confirmed!

Colbert isn't really a Republican.
Think about it.
 * Colbert, not Republican? You'll never get people to believe that.
 * That's ridiculous, Colbert wears glasses! And, uh...hmm.

Sweetness talking is a long-running gag by The Colbert Report staff and a corrupt surgeon.
They had a remote-frequency hearing aid powered by one of those tiny, movement-recharged power cells inserted into his deaf (or deafened) ear, and whisper into it whenever he is holding the gun. Fortunately, their plan to get him to ignore gun safety backfired when it ricocheted off his balls,

Colbert is actually reasonably conservative,

 * He just has a sense of humor.
 * This one is true! Sort of. Colbert isn't conservative in the modern political George Bush/Dick Cheney sense, but he does admire Reagan and (pre-Watergate) Nixon on personal levels. He owns a 1968 Nixon campaign poster and a dog named Gipper.
 * I think the dog belongs to the character. The poster is his though!

Colbert is ACTIVELY working to eradicate all species of bear on earth.
Think about it... Remember how he replaced his stage manager Bobby specifically for global warming? That's for the polar bears. Grizzly bears, the terrible beasts they are, were the reason he and Jon Stewart (who is obviously in on it too) worked so hard in Barack Obama's favor. With Sarah Palin stuck in Alaska, she has nothing to do but kill bears.

His most sinister work is the panda. Stephen has laced all bamboo everywhere with chemicals to reduce the panda's sex drive. Because honestly, whether it saved their species or not, would you want to see two pandas humping? I wouldn't.

Stephen is already on a team for the 2010 Winter Olympics
It's just a secret and wont be revealed until he tries out for the sport he's actually competing in.
 * Called it? Maybe? We don't actually know when he 'joined the speed skating team', but...

Stephen died as a result of one of many Prescott Pharmaceuticals' products.
As of January 12, 2010, his cell phone alarm is the Dead Like Me theme. He was obviously the last reap of one of the Reapers, and either has been Undead All Along or found a loophole in the swiss cheese memory clause. (Now... how to use this fanitude to aim the Colbert Nation to the desired result of a Dead Like Me revival?)
 * When Gary Sinise was being interviewed, he asked Stephen what that thing was on the left side of his mantle. He was referring to the western statue with the horses, but Stephen thought he meant the hourglass on the far left. Stephen commented, "That is an hourglass. It was a gift from the grim reaper." Note that all the sand was at the bottom part of the hourglass.

Stephen Colbert wants an iPad.
Okay, I know this is kind of out there, but go with me on it. Although Colbert doesn't like to read, he does like shiny things. And what's more shiny these days than an a gigantic iPhone? GIVE STEPHEN COLBERT AN IPAD.
 * As of April 1, 2010... CONFIRMED! (It even does salsa)

Stephen possesses a working Prose Portal.
However, he apparently only uses it to travel to comics, since he doesn't like to read. He looks exactly like Tek Jansen, and (based on the Cheating Death segment from March 24, 2010) has acquired and re-programmed Ruebert, using his incessant whine for good instead of annoyance. This may also be how he "wrote" I Am America and So Can You: The entire book is a quote of him shouting (and not typing) it, just with the quote marks bumped down one level and the dialogue tags turned off.

Stephen has a Split Personality.
The "normal" Stephen, and the Stephen we see on the set, are two separate minds in the same body.
 * Confirmed as of April 22, 2010. After flat-out refusing to interview the stand-ins for Gorillaz, he made his real self change clothes and do it for him while he sat pouting in a corner of Steve's brain.

Stephen's I Am America (And So Can You) is a homage/challenge to America.
His glorious "stack of paper" proclaims a self-portrait with the subheading "America." Somehow, he's apparently trying to call the bluff of a certain Alfred F. Jones.

Conversely, Stephen IS America.
Ever seen those petitions to have Stephen Colbert voice America from Axis Powers Hetalia? He won't have to since he's pretty much Alfred in a dyed wig. I mean, he's hyper, brash, uber-patriotic and loves burgers and apple pie. He got his hatred of bears from a bad visit to Canada.

Stephen got his hatred of bears by playing Banjo Kazooie as a child and not being very good at it.
...Nope, me either.
 * The biggest problem with this is that Banjo Kazooie was released in 1998. But then again... Time Lord.

We are all Stephen Colbert in Purgatory.
You mean heaven, right? The guy has the greatest life ever.

Sam the Eagle is Stephen Colbert's fursona.
Stephen's enough of a nerd that he might have created his own anthro mascot character at some point in the past, and the two do have a suspicious amount in common.

After seeing the previews of the new Captain America movie Stephen will do something with that shield.
You want it to happen.
 * Jossed.

At one point in time the wheel of heroes has/will say Alfred F Jones.
Either as a reference to Stephen calling himself America or because America really just likes him that much. When his name goes past, Stephen will stop talking and watch it cross the screen, mumble something about plans, and snap back to what he was doing.

Stephen is the creation of a union between Alfred F Jones. and a Timelord.
(Spoilers for season 6 of Doctor Who) Conceived in the TARDIS, Colbert is the child of a Timelord and America, but because he was conceived in the TARDIS, and thusly near a time vortex, he has the traits of a timelord while still being the child of a nation. Also, because he is the child of a nation, he has an innate need to be a nation- hence the title of his website as Colbertnation.