The frequent Imagine Spot moments JD has are real and JD imagines that they never happenedExactly What It Says on the Tin
Sacred Heart is in San Antonio TexasMy 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.
Sacred Heart is in Sacramento, CaliforniaNot 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)
Scrubs is a sequel to The Adventures of Pete & PeteJD 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 imaginationPerhaps 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.
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.
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 StevenThe only evidence for this is that that's what he called Rowdy's replacement.
The Janitor's real name is Jan Itor.Why would he give a fake name at his son's career day?
The Janitor's name......starts with a "Ch" or a "Sh". As seen in the second half of the Bahamas two-parter.
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.
All of this speculation about the Janitor was put here by the Janitor himself to seem more mysterious.
Dr. Cox's pessimism is the result of a life-altering disillusionmentIn 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.
Dr. Kelso is a KiraOkay, might be a stretch, unless someone can find proof.
J.D. is the Janitor's insane work-buddyThat'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 showYou 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...
Denise is the reincarnation of Cutthroat Bitch from HouseBecause....Yeah.
The Janitor is... Neil Flynn fallen on hard times.This was heavily implied when J.D. recognized him while watching The Fugitive.
The Janitor used his taxidermy skills to make a Neil Flynn skinsuit that he wears 24/7.
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 GalacticaGaius 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 2Originally, 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.
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.
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 nameThe Name being Glenn Anthony/Thomas (Depending on whether the intern said Tommy or Tony) Ephraim Klaus Nigel Joshua (insert Asian Name here) Matthews 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.
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 ancestorSee 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...
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.
At least one incarnation of the Brain Trust represents the Four Horsemen of the ApocalypseOK we have it like this
The Janitor is secretly the chairman of the board of directorsHe 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.
The world is viewed through JD's/Lucy's eyesThis 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).
My Fallen Idol is the true last episode of Scrubs
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/sisterIt 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).
"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.
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 LordThe 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  that has many of the traits of both JD and Elliot. She is prone to , 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.
Denise Mahoney is actually Jennifer Dylan Cox, also back in time.If time travel is possible in the future, then why not? She has traits of both Jordan and Perry Cox, being brilliant and abrasive. She was first introduced as "Jo", but later on she's called "Denise", her father in the future told her that if she wanted the best possible mentoring experience, that she should learn from the best other doctor he ever knew.
Doug Murphy was only allowed to treat patients who were dying anyway.Ignoring the sitcom staple of having a guy in the same job as the protagonist and failing miserably, the is no way Kelso would settled any legal actions against the Hospital for an intern that inept. What was really happening is that he was knowledgeable enough to look like he was trying to be a better doctor, while Kelso stuck him with patients that were dying anyway and draining hospital resource. The hospital drags it out for as long as they can(even making him repeat a year) but it had to end sometime. Luckily all that experience with causes of death trained him to be an excellent coroner. And because they know Doug is not bright enough to catch on, they never had a gurney for the various bodies he totes around the just say they do, then when they chase him off to go collect a body they move the gurney back to whoever was using it before their ruse.
Doug Murphy is an "Angel of Mercy" serial killer whose homicides are written off as incompetence.He is excellent at appearing to be upset about the deaths that occur under his care, but in actuality it's a cover. He comes under immense pressure as soon as he begins his internship and is tortured ceaselessly by both Kelso and Cox, leading to a psychotic break early on that expresses itself as mercy-killing. At the same time, his "nervous guy" persona enabled him to believably cover up the deaths, and he simply appeared unsuited to be a doctor, instead relocating to the morgue, where he seemingly regards cadavers as lumber rather than people.
Laverne and Snoop Dogg Attending made out at her above-ground-pool party.In the episode "My Cuz," there's a one-off joke that Snoop and Beardface were "wiener cousins" through Nurse Roberts. A found it a bit disconcerting, because Laverne was married and probably had been for a while, seeing as they had a teenage son — maybe the thing with Beardface happened before she got married, but she and Snoop couldn't have known each other very long because he was an intern at the beginning of the series. But then I remembered that she was having some marriage troubles with her husband in Season 4. It could very likely have been thanks to Snoop. It happened at the pool party because all of the Noodle Incidents happened there.