Scrubs/WMG

Sacred Heart is in San Antonio Texas
My girlfriend's theory is that it's in San Antonio because in the episode where Dr. Clock (Heather Graham) has her watch set to the time in Greenland, Elliot states that it's 3 hours off. Also Shaun works at Sea-World. The only Sea World in the proper time-zone? San Antonio.
 * Elliot once has to take a train to see Shaun in Sea World. There are trains servicing San Antonio, but it suggests that Sacred Heart is somewhere else in Texas at least.

Sacred Heart is in Sacramento, California
Not the wildest mass guessing but hey South Sacramento is the only place you can get Dunkin' Donuts in the state. (As Turk did in one episode or another)
 * Also 916 as in (916)-CALL-TUR is the area code for Sacramento.

Scrubs is a sequel to The Adventures of Pete and Pete
JD is Big Pete. Cox is Artie, traumatized by having joined the adult world without his superhero persona. The Janitor is Endless Mike Hellstrom, only grown up.

JD's fantasies are hallucinations.
Or at least the fantasies he confuses with reality are. Numerous times, he has disconnected with reality enough to make strange movements, leading other doctors to ask, "Are you okay?" In the fairytale episode, he asks Elliot, "Am I imagining him?" This is presumably because he was born prematurely, as evidenced by his reply "I was a preemie" when a patient notes that he is a "strange man."

The entire world is created by JD's imagination
Perhaps he's in a coma. Perhaps it's a really long daydream. But what if the voice-over JD is the real JD's mind commenting on this entirely new world created inside his head, where he looks at himself from a distance? JD seems to be aware of some things that the characters should not hear, like the incidental music. And voiceover JD (or Real JD) seems to be aware of and comments on scenes that JD doesn't witness. Basically, what we think is JD thinking inside his head, along with the various voiceovers, is the voice of Real JD's mind; everything we see and hear outside of that is simply a construct created by Real JD's mind.
 * Impossible. He's not nearly autistic enough.

The Narrator from the It Just Bugs Me page is The Dark Passenger.
It can go to different people, such as in "His Story" and "Their Story." Perhaps it just grants limited knowledge of things nobody else on the show could know and gives the host strange fantasies.

Jordan is the ancient demon-mother Lillith in disguise.
Look at the evidence! She sleeps with anything, hates humankind in general, and somehow never looks quite right despite her purported attractiveness.
 * You don't think Jordan's hot?
 * Oh, Jordan is hot. She just always gives me a "bad feeling about this". -- Eli

Jordan used to be Kate on The Drew Carey Show, but she killed The Devil, got his powers, and decided to move to California when her double life got boring.
As soon as she got The Devil's powers, she made an illusion of him that required a virgin bride (The Devil wanted a slut) and reverse-engineered a second life as the daughter of a dying hospital director in San Frangeles. When Jordan!Kate got tired of Drew, she had Kate leave Cleveland. She spent the next seven years trying to usurp Kelso's position as resident life-force stealing demon.

The Janitor's real name is Steven
The only evidence for this is that that's what he called Rowdy's replacement.
 * His name is Josh. He tells Cox this while defending the integrity of his newsletter.
 * I think it was mentioned somewhere that JOSH actually stood for Janitor Of Sacred Heart?
 * The Janitor enjoys lying to people and constantly tells contradictory stories about himself. If he said it's Josh, then it probably isn't.
 * Considering how Janitor was treating Steven as though he were alive, it seems more likely that the person that made him had named the dog Steven, not him.

The Janitor's real name is Jan Itor.
Why would he give a fake name at his son's career day?
 * We can't even be sure his son is real.
 * Alternately, John 'Itter. He's JD's father.
 * He does make that claim in Season One.
 * It's not Jan Itor, it's Thejan Itor.

The Janitor's name...
...starts with a "Ch" or a "Sh". As seen in the second half of the Bahamas two-parter.
 * Shaun Itor?

The Janitor's real name is Neil Flynn.
That's right! Neil Flynn is played by...Neil Flynn. JD noticed that the Janitor played the transit cop in The Fugitive, and the Janitor did confirm it. So, if the Janitor played the cop, and that cop was played by one Neil Flynn, then this means that the Janitor and Neil Flynn are one and the same.

The Janitor's name is Neil Flynn...
Who is working at Sacred Heart under the name John 'Itter, who is JD's dad.

Dr. Cox's pessimism is the result of a life-altering disillusionment
In one episode, his mentor comes to the hospital, and Dr. Cox acts towards him a lot like JD acts towards ol' Coxy. So, somewhere between the time he was a fresh-faced Billy Idol-impersonating intern and when we met him as a hard-minded no-nonsense attending physician, he became so traumatized by something that he lost all faith in life. That's why he's so hard on JD - he sees too much of himself in the younger man, and he's scared the same thing will happen to him.
 * I thought that was Canon?

Dr. Kelso is a Kira
Okay, might be a stretch, unless someone can find proof.
 * If he was, then his wife would probably be dead by now.
 * Unless his wife is his Shinigami! How about that?
 * So THAT'S why we don't see her! We haven't touched her note! Shinigami probably can't reproduce under normal circumstances, but Kelso's son should still be half-shinigami; a gay half-shinigami works due to Rule of Cool.
 * Maybe he killed TCW and Dr. Miller.
 * Dr. Miller, no question about it. But why would he go after TCW?
 * Because he's a Magnificent Bastard?
 * Because her husband had an odd insurance plan that cost the hospital a lot of money to keep him in the room. Kelso IS a spendthrift.

J.D. is the Janitor's insane work-buddy
That's why the Janitor hates him. J.D. makes his life a living hell by being a special-needs crazy person. The hospital is real, mind-you, but all the bits about J.D. being a doctor are just parts of his hallucination. Turk, Carla and Elliot tolerate his hanging around because they feel sorry for him. This is why J.D. can get away with crap that would get him fired as a doctor...

Scrubs is upstairs from Chrichton's ER television show
You never see the emergency room in Scrubs. That's because it's an entirely different show called 'ER', and it used to have Clooney beating up pedophiles like God intended...
 * No, the Sacred Heart ER is where George Clooney's character went after he left the show ER. (ER was set in Chicago.)

Denise is the reincarnation of Cutthroat Bitch from House
Because....Yeah.
 * That would require Denise to have time traveled. Their lifespans overlap, and CTB's timeline is almost certainly linear. So Denise was born around March 2009 and then travelled back in time before she went into premed.

The Janitor is... Neil Flynn fallen on hard times.
This was heavily implied when J.D. recognized him while watching The Fugitive.
 * They just incorporated it into the back story for Janitor. It isn't supposed to imply that it is Neil Flynn himself.
 * Hey, if it could work for Creed Bratton...
 * So the Janitor left so he could star in The Middle?
 * To me he did.

The Janitor used his taxidermy skills to make a Neil Flynn skinsuit that he wears 24/7.

 * Have Neil Flynn and Janitor ever been seen in the same place? It could be that Janitor completely replaced him, taking acting jobs to supplement his (formerly) incredibly low janitor pay, when he isn't hanging around the hospital and tormenting JD, or courting Lady.
 * In one episode, JD gets ink on the Janitor's skin (due to a faulty ink pen). When the Janitor points this out he says, "This is my favorite skin!"

JD contracted a degenerative disease of the brain at some point, possibly from a patient.
Notice how he seems to get dumber & more emotionally unstable every episode.

JD is the ancestor of Gaius Baltar from Battlestar Galactica
Gaius Baltar Compare to: JD

The hallucinated Cylon that Gaius sees is clearly an inherited trait and originated with JD's fantasies. It was already shown that JD's baby does the daydreaming thing, and so it is a genetically inherited trait. It would just become more refined over the intervening generations before Battlestar Galactica until the hallucinations tie into reality, and comment or give advice on the current situation.

Either that, or they are the same person and JD/Gaius is a Time Lord.

If they are the same person, and he is a Time Lord, then the contrast between their personalities could be explained as the intervening centuries, along with the destruction of Caprica, to have matured JD somewhat.

Sunny will be the next Nick Murdoch (broken intern from season 1).
She's happy, optimistic, and under a lot of stress; and she keeps getting paired up with Denise, who quite frankly scares the living daylights out of her. She's stayed up for days trying to take care of patients to the point of hallucination. Unfortunately for her, the cuties must be broken. She'll snap, and the only thing that'll save her is not being the best intern so that she's still friends with Denise and... whoever's in charge of her.

Nick Murdoch is Matt Murdoch's half-brother.
Vague resemblance, but not enough to be a clone. Nick will try another line of work but, being irreversibly broken, he'll eventually be sent to Arkham (remember, in WMG world, DC and Marvel are in linked continuities). There, he will take on the technology of his cellmate and become The Doctor (supervillain name, not the Doctor you're thinking of). On a visit to California, Matt will stop him from destroying Sacred Heart, along with Janitor and his friend and former co-worker Harrison Ford.

Nick Murdoch is Jack McFarland.
They both are played by the same actor for a start. The timelines do also work, if you assume Nick/"Jack" (most likely an assumed name to get into college parties) studied medicine. At some point between a year after Will came out to Grace at Thanksgiving and the very 1st episode of Will & Grace, Nick graduated, abandoning the overly camp persona to focus on his studies, and then transferred to Sacred Heart. The events of My Super Ego happened, and Nick subsequently underwent a massive breakdown, his mind snapping back to the last point in time when he was happy: being "Jack". At this point he moves back to New York, moves in with Will, and the events of Will & Grace occur. This explains Jack's lack of maturity (his mind snapping back to a point before he matured and focused on his studies), his overly gay attitude (it was deliberately over the top when he did it the first time), and his nursing aptitude (his medical knowledge and skills shining through). His family play along, naturally, and Will and Grace don't know about Nick. Karen may actually know, between her private detectives and her comment about talking hundreds of times on the phone but never actually meeting (until the 1st episode of Will & Grace), but if she does she's not telling. It does explain why she spoils him far more than her step children though.

The Janitor didn't exist before Season 2
Originally, he was just JD's imagination. But after JD constantly referred to "the janitor", even though the real janitor only showed up at night, eventually people believed that there was a day janitor; and so he became real. This is also why the janitor can't be fired; he doesn't exist on any hospital staff list, and the higher-ups haven't heard of him.
 * So this universe operates on Clap Your Hands If You Believe logic? I'd come up with a witty retort, but that sounds awesome.
 * According to IMDB:
 * Through the first season, the cast and crew, especially writer/creator Bill Lawrence, were so sure that the series would be canceled by the end of the season, that a plot twist was created for use when they'd have a forced series finale. This plot twist noted the fact that the Janitor, Neil Flynn's character, never directly spoke nor was spoken to by any other character than JD, Zach Braff's character. Therefore, the Janitor would be a complete figment of JD's imagination. This idea was kept up into the second season, still in fear of cancellation, until Flynn asked Lawrence to be able to finally interact with another actor on the series. (Although Elliot actually throws a cup at him in the 6th episode and sarcastically says "SORRY!", in episode 11 he gets punched on the balls by a little girl and in episode 15 the janitor teases the nurse with the vacuum cleaner)
 * Also in the first episode with Ben, he shows JD photos where the Janitor is in the background and asks who he is. But it's strange that Ben could see The Janitor on the photos but never in person. Hmmm...
 * The Janitor is obviously a reverse vampire, you can see him in mirrors and in photographs but not in person.

Janitor is an archbishop.
Not necessarily of the Catholic Church or even any mainstream religion. The second time the "Minister of Justice" that Todd found tried to say his name, it sounded like "Archb-". It could be that he hadn't said the Janitor's name at all, but his title, preceding the name.
 * Maybe his name is Archibald.

Janitor is a superhero.
The Janitor. Either one of the darker, gritty ones from the eighties, or a villain. He wanted a new Janitor outfit with a cape from Kelso to replace his old one, which had been damaged or sucked into a plane engine. His backstory confusion is so nobody will believe him if he accidentally gets hit with a truth ray or truth serum. His motto is either "cleans up crime" or "he'll clean out the banks and clean your clock, but won't clean anything else"; and his catch phrase (good or evil) is "I'll mop the floor with you!" Also knows Daredevil's previously-unknown twin Nick Murdoch from his days at the hospital, and saved or threatened Harrison Ford, getting him a part in The Fugitive.

Janitor has never intentionally killed an animal.
He bought Bingo (the salt-and-pepper dispensing rabbit) and Stephen online. He stated outright that he traded his squirrel army for a stuffed dog he found online, and may not have been lying. The squirrels were all captured alive, and he could have either been really bad at taking care of squirrels, or trained them to stand really still on a plaque or stand like he did with Sancho (the raven) to make Kelso think he'd been killed and stuffed.

Janitor has a very long name
The Name being  Thus his comment that the many names he's been called all have a dagree of Truth to them

JD's fainting spells are also triggered by ImagineSpots.
Not just defecation. But it's a different trigger that locks his knees instead of falling over. Or something.

JD is a repressed Bisexual.
Notice that, during his numerous moments of Ho Yay, he barely narrates. JD is an Unreliable Narrator, and so he glazes over the stuff that he's not comfortable with.
 * This is true, but there are no real Ho Yay moments; they're always one-sided. JD is almost always the instigator. The Todd may wear man-thongs, but he never tried to have a long sensitive talk with his best friend while exchanging hand-made gifts.

JD is the future Milhouse.
They're both nerdy, kind of whiny, effeminate at times, and not particularly bright. They also almost have the same hairstyle.

Gaius Baltar is JD's ancestor
See the other JD/Baltar theory and the finale of Battlestar Galactica for details. Done right, this could even be a Stable Time Loop.

The Janitor is a Shinigami and Doug Murphy is his Kira.
Janitor "auditioned" J.D. for the post of his Kira in the first season, but J.D. was too nice. Eventually he found Doug, who "everybody knows" is just a horrible doctor who is responsible for a boatload of deaths in the hospital and who somehow knows exactly how everybody in the morgue has died. Doug likes to tear pages out of Death Notes and put them into patient charts. Sometimes he has fun...
 * "Patient X. Latex glove sewn in body during surgery, causing infection.
 * "Jill Tracy. Rabies."
 * "Mr. Bradford. Rabies. Jill Tracy's rabies-infected heart valve transplanted into body."
 * "Ben Sullivan. Cardiac arrest following examination for leukemia."

JD is Shinji Ikari and the whole series takes place during Instrumentality.
Because the only person more whiny and pathetic than JD is Shinji, this is the closest he can come to being a success. Dr Cox is a softer version of Gendo (JD and Shinji both want that illusive hug), Kwarou is Turk, Jordan is kinda a gestalt version of Akagi and Misato, Elliot is Asuka, Carla is Yui, Ted and The Todd are Kensuke and Toji, Rei is Kim, and the Janitor...well he is Shinji and JD too.

The Janitor is a Changeling.
Specifically, a Wizened Drudge. (see Winter Masques) It explains his strange powers, lack of background (taken by some Fetch probably, and who knows what he did with that), craziness and disrespect of authority, and being able to do his job so well when nobody's looking.

Of course then it's completely certain that the rest of the cast are various other New World of Darkness inhabitants.
 * So close. In fact the Janitor is a changeling. Specifically, he's the Changeling who was once Neil Flynn. That guy in Mean Girls and The Middle is a fetch.

At least one incarnation of the Brain Trust represents the Four Horsemen of the Apocalypse
OK we have it like this


 * The Janitor: War his thing with JD and his general sociopathy
 * Ted: Famine his generally worn and neglected nature,
 * The Todd: Pestilence just how much of a metaphorical "plague" he is to his co-workers
 * Doug Murphy: Death. considering the fate that most of his patients met and the job he took after he quit being a doctor

The Janitor is secretly the chairman of the board of directors
He never gets into any trouble, comes and goes as he pleases, drinks on the job, and getting fired had no effect on him. He's friends with Kelso at night. He certainly doesn't do any cleaning. On more than one occasion, he has been able to manipulate Kelso in a way that indicates Kelso has to go along with it, because the Janitor is his boss. He consistently lies because to tell the truth in any way would reveal who he really was. He hangs around in the guise of the Janitor so he can keep a closer watch on how things are going in his hospital.
 * Interesting since we never see the rest of the board, we only hear about them. He probably doesn't sit in on the meetings either, and just relays his instructions to Jordan or one of his other lackeys.

The world is viewed through JD's/Lucy's eyes
This would explain why Dr. Kelso goes through Villain Decay: he starts out as the evil overlord, generally becoming less scary as JD gets more experienced and he realizes that Kelso is a cake-loving moron. This is also why Kelso has such Character Derailment in the last season: He's gone from being the resident villain (JD's point of view) to the old, retired doctor with dated ideas about medicine (Lucy's point of view).

The last season didn't actually happen.
At least I hope not. It was terrible.

The Todd was sexually abused by both his father/uncle/brother and his mother/aunt/sister
It would explain why he seems gay sometimes (because he was abused by a male family member) and straight the rest of the times (because he was also abused by a female family member).
 * Wow. Talk about Unfortunate Implications with this WMG.
 * Or, y'know, he could just be bisexual or pansexual.

"Guy Love" wasn't a Hallucination.
J.D. and Turk were just so excited by the idea of the patient's brain interpreting everything as song that they actually broke out into song. Which is why it is the only song from the episode to be referenced later.
 * Yes. They wrote it idly, years ago, but knew they would never be able to preform it in front of anyone without being horribly ridiculed. Then this chance came, and they seized it.

The Janitor from this series and Clone High are the same and he regularly jumps back and forth between the two.
All the stories the he tells are actually true, but they occurred in the bizarre world of Clone High. The Janitor's occasional misanthropy is his disappointment with the cruel nature of the hospital.

The Janitor is a Time Lord
The parallels of the name are obvious, as is the way he gets away with anything and everything. Either the cart of the van is his Tardis. He may actually have a sonic screwdriver, or at least a sonic mop.

Lucy is JD and Elliot's daughter, and she's gone back in time.
Think about it. She's a Composite Character that has many of the traits of both JD and Elliot. She is prone to Imagine Spots, is overly nuerotic and screwed up with relationships. Why else does she get along so well with the two of them and always runs to them for help. She decided to be a doctor too and after finishing med school decided to intern when her parents were still young doctors. Note also that she calls Kelso's idea's about medicine dated.
 * It also explains why Elliot took such a liking to her so quickly. "You're like the nice sister I never had," she said.