These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Some of the fanbase speculates that Dr. Cox is Jerkass to JD partially because he doesn't want JD to idolize him as he sees himself as a terrible role model.
Award Snub: Other than Zach Braff, none of the cast were nominated for an Emmy or Golden Globe. Particularly infuriating since John C. McGinley has had some of the most phenomenal, intense scenes on the show.
Case in point: The ending of "My Lunch". How the HELL did that not get him an award or at the very least, a nomination? Sure, his competition were heavyweights like Steve Carell, Alec Baldwin, Larry David and Bryan Cranston, but in 2006 Kevin James managed to get a nomination for King of Queens.
And Speaking of Braff, he only got nominated for a single Emmy during the entire run of the show.
Broken Base: Season 9. Either the worst thing to happen to the show, or a decent season brought down by Fan Dumb and huge expectations. Some fans look at it not as a Scrubs season, but a Spin-Off like Bill Lawrence originally intended.
Crack Pairing: Unusually for this trope, Elliot/Janitor is actually a recurring arc which is explored with genuine depth and sensitivity, despite the fact that it never really goes anywhere.
Critical Research Failure: For a show that is usually really good about being factually accurate their portrayal of Turk's Diabetes is shockingly ill-informed. Aside from the unlikelihood of a person like Turk developing Type 2 Diabetes, which is usually the result of prolonged obesity, the show treats the illness as if it were basically AIDS - a guaranteed death sentence. At one point Turk even gives a dramatic speech about his Diabetes, musing about how old he'll be when it takes him. In real life Type 2 Diabetes is not only easily survivable with many diabetics living long and successful lives, but it is in fact even potentially reversible.
The ending of "My Philosophy" where most of the cast joins in for the song "Waiting For My Real Life to Begin".
In one episode, a patient wants desperately to be able to perform with his band, which the doctors assume is some drunken garage metal band. At the end of the episode, it turns out his "band" was The Polyphonic Spree.
Ted and his band singing the theme song to "Underdog" during the last moments of "My Hero".
Ted and his band singing "Eight Days a Week" at Turk and Carla's wedding. Awesome.
Ted's acoustic cover of "Hey Ya" in "My Soul On Fire".
To make it easier: ANY time Ted and his band (The Worthless Peons) sing.
Fan-Preferred Couple: JD/Cox is the most popular ship in the fandom, despite the fact that JD and Elliot end up together and Dr. Cox has been in a stable relationship with his ex-wife since season 2. It's also kind of ironic because canon-wise, JD and Turk are the ones who have a lot of Ho Yay.
Believe it or not, JD/Elliot fell under this for a time. Bill Lawrence has stated that the end of the third season was supposed to definitively shut down that relationship. He eventually caved under fan pressure, adding more Ship Tease between the two in later seasons and having them get back together in the eighth season.
Fountain of Memes: The show in general qualifies as this, but Dr. Cox alone has to go down as one of the biggest meme generators in all of sitcom history.
"Funny Aneurysm" Moment: John Ritter's line in his guest-star appearance: "I'd love to go to your lecture on heart murmurs! I'm a big fan of those things!"
One wonders how comfortable Phill Lewis felt about having to read Hooch's line where he threatened to mow people down in his car. Lewis himself in the early 90's had spent a year in prison for accidental manslaughter after causing the death of a young woman whilst driving intoxicated.
Gratuitous Special Effects: There was an Imagine SpotOnce an Episode that often featured somewhat elaborate special effects. For instance, in an early episode, JD imagines that his head blows up in a scene that would be more appropriate in a horror film, not a comedy/medical drama.
Growing the Beard: Season 8 was almost universally praised as better than the previous seasons. Better plots, stronger acting, and some really great episodes made this season a great end to the show, despite what season 9 may say...
Also, in season 8 JD did in fact grow a beard.
Harsher in Hindsight: The season 1 episode "My Old Lady" is already a Tear Jerker. But Kathy Joosten, now passed away, makes it an additional punch in the gut.
Season 4 had Dr. Cox taunting JD over the fact that every doctor will eventually be responsible for the death of a patient. Every doctor expect Cox, who is "the exception that proves the rule." Watch this back to back with "My Lunch".
Hilarious in Hindsight: The Janitor suggested in the episode concerning the Iraq war that they should look for Bin Laden in Pakistan. Lo and behold, several years later...
In "My Hero", JD sings the praises of Tony Shalhoub for his performance in Wings. Shalhoub later went on to win an Emmy for Best Leader Actor in a Comedy Series for his role in Monk, beating Zach Braff who was also nominated for that category. This lead to his declaration in "My Own Worst Enemy".
During one of Dr. Cox's epic rants, he names Hugh Jackman winning an Oscar as one of the worst things that could possibly happen in the world. Now in 2012 with Tom Hoopers's big budget adaptation of Les Miserables (2012), many critics are placing Jackman (playing Jean Valjean) at the top of their lists for potential Best Actor nominees/winners.
The episode My Way Home, which parodied The Wizard of Oz, and was directed by Zach Braff is an interesting case. Come 2013, and Braff co-stars in Oz: The Great and Powerful.
In "My New Old Friend," Kelso tells Turk that he needs to remember that "everybody lies" when they're speaking to a doctor. A year later, this would become the catchphrase of another misanthropic doctor.
Ho Yay: JD and Turk, Elliot and Carla, JD and Dr. Cox, JD and many male guest stars, Elliot and many female guest stars.
With JD and Turk, the Ho Yay is so blatant that some characters initially thought they were gay. Carla once commented that she hoped she might be as close with Turk as JD is, one episode after she and Turk got married.
Dr. Kelso has the occasional mention of his days in the military. The name Johnny is tattooed on his arse (but he insists it's "a Navy thing, you wouldn't understand")
The Todd has more than a few elements. Especially his love for banana hammocks.
In the episode where everyone imagines being married to Elliot; Turk and Carla have a disagreement and Carla imagines drinking wine with Elliot who wants to lay off some steam by going shoe-shopping, Carla however wants to have tender emotional sex and then cuddle and THEN go shoe-shopping, they share a kiss before the scene cuts back to Carla saying "Life would be so much simpler..."
Elliot would go gay for Jamie in Pediatrics, as would (apparently) all the other women at Sacred Heart.
Magnificent Bastard: The Janitor, Dr. Cox, and Dr. Kelso. Yes, this show has three of them. The best part? They will occasionally engage in a battle of wits.
Turk dips into this during My Turf War.
Marty Stu: Massively deconstructed with Dr. Kevin Casey, whose general Stu-ish-ness in all fields, from medicine to surgery to knowing what's wrong with the oatmeal, comes from the fact that he has OCD so severe that he can't stop himself from compulsively obsessing about everything and re-reading things hundreds of times over until he knows everything about everything, which comes at the cost of being able to function normally.
Mary Sue: Kim could be considered a parody of one due to how she was inserted into scenes that happened before we even met her character; a series of flashbacks showed her with JD and the others at various important plot points throughout the series. The fact we didn't see her the first time around was explained by the fact that JD apparently can't see women who are wearing wedding rings.
Played Straight with how apparently 'everyone' in the hospital loves her, including the men, the women, and the greasers. Then there's the fact she only wore her wedding ring because she was tired of getting hit on all the time. It's hard to believe that she could have been such a popular character when we've never heard of her before.
Though it was also stated that the reason she was liked by everyone was because she never does anything that might offend anyone, which might go some way to explain why she wasn't that noticeable.
Kim even fixes the x-ray image at the title screen, because it was the wrong way around and had been 'bugging her for years'.
Nightmare Fuel: Baby Sam's daydream. Kelso and Turk with boobs. Nuff said.
As a more serious example, there's the episode where Turk does a surgery on a patient who opted to use hypnosis instead of anesthesia. Everything appears to be going fine, but then the patient's eyes open... oh God, that scream...
Relationship Sue: Julie from Season 5. She's essentially there as a Distaff Counterpart to JD and they hit it off immediately in the first episode. Then it gets subverted in her second where JD realises she only sees their relationship as a bit of fun, while he wants serious commitment. The Irony of her being the only girl JD had good reason to break up with is lampshaded.
The Scrappy: Carla isn't well liked in some fandom circles because of how bossy she is, and how demeaning and unfair she can be to Turk. In fact both her and Elliot are often disliked because they get away with anything and everything with little consequences.
For some, JD in later seasons.
Kim. Mostly due to the fact she lied to JD about miscarrying their child just because she didn't think a relationship would work between them. The fact everyone seems to sympathize with her over JD doesn't help.
Ed the intern. Many were relieved when he was pulled from the show due to his actor having commitments with another network.
Although in that case he clearly wasn't meant to be liked.
Cole from Season 9, for being damn near exactly the same as Ed, but given more focus. They tried to make him sympathetic by giving him cancer for one episode but it didn't work
Dr. Miller was introduced in season 3 as Turk's personal "Dr. Cox." Unfortunately, she had all of his Jerkass qualities with none of the Pet the Dog moments and she was promptly written out of the show after her one season.
Carla's brother was also introduced around the same time as a massive Jerkass towards Turk for almost no reason, and unlike The Janitor, his actions come off as mean-spirited rather than funny. Like Dr. Miller, he didn't last long in the series either.
Turk mistook him for a valet at his mother's funeral, complained about him not knowing english when he only knew a few words of Spanish, forgot to pick him up at the airport, and questioned his masculinity for liking When Harry Met Sally so it's more of a case of Jerkass Has a Point.
Jimmy the Overly Touchy Orderly.
Seasonal Rot: Seasons 5-7 are generally considered this, though opinion varies on when precisely it set in (halfway through Season 5 is a popular choice) and how bad it actually got. The show leaned more heavily on Imagine Spots, quick gags, cheap jokes, and many of the plotlines fell flat; Season 7 in particular suffered from being cut short by the WGA strike, which prevented many of the planned storylines coming to fruition, along with the network airing the episodes out of their intended order. That said, season 8 is generally considered one of, if not the best, season of the show.
And of course, some fans claim that Season 9 is so awful that they're willing to defend seasons 5 to 7 despite having ragged on them earlier.
Some Anvils Need to Be Dropped: No one is perfect and even the best of us mess up in a while. The show is in no way subtle about its Aesop, but it's pulled of with the right blend of pathos and humour that it never becomes grating.
Well, that explains the lyrics to the theme song: "I can't do this all on my own/Oh, I'm no/I'm no Superman."
A lot of the patients are woobies, below are some examples.
Brian Dancer, a soldier who was injured in Iraq whose injuries were too severe for him to continue to serve in the army, which was the only place he felt at home. Even worse, he has the Unfortunate Name of Private Dancer.
Elliot's patient Shannon in "My Number One Doctor", she's paralyzed and it's getting worse and worse to the point that she'll be trapped in her own body and unable to move in the slightest and there's no cure.
George, a patient in Season 8 who is dying and has no one to be there with him as he dies, so J.D. and Turk stay with him.