Implied but not seen in season 6's "My Cold Shower"--while imagining what being married to Elliot would be like, Dr. Cox pictures her freaking out over the order of a cracker stack two days into the marriage. He's seen gripping a knife tightly, then it cuts to him being escorted away from a crime scene with a big grin on his face.
Jordan's brother, Ben, in his first onscreen appearance convinces JD he's been admitted for a construction accident. He shows off a bloody nail through his palm, which looks real enough to make JD pass out.
Season 5 episode "My Five Stages"--Dr. Kelso's hatred of bicycles is explained in a flashback where his father uses young Kelso's bicycle to leave the family forever.
Mentioned by both Dr. Cox and the Janitor, but not seen.
In season 5's "My Transition," the Janitor gifts Carla a "babycage", which is essentially a dog kennel. He says it's a joke when people react negatively, but a later phone call to his mother ("No, Mom, 'baby cage' and 'playpen' are NOT 'potato, po-tah-to!'") implies he really was kept in a dog kennel as a child.
Another season 5 episode "My Half-Acre," sees Dr. Cox claim that his father showed love by "purposely missing when he threw bottles at [his] head".
Implied but not seen in season 6's "My Cold Shower"--while imagining what being married to Elliot would be like, Dr. Cox pictures her freaking out over the order of a cracker stack two days into the marriage. He's seen gripping a knife tightly, then it cuts to him being escorted away from a crime scene with a big grin on his face--the sequence is played for laughs and goes by within about 15 seconds.
Turk and JD keep a taxidermied Golden Retriever in their apartment starting all the way from the beginning.
The Janitor has squirrel taxidermy as a hobby in later seasons--he turns them into things like pencil cases. This is played for laughs.
There is a scene where someone sort of does this to themselves but it’s a minuscule amount of dirt they barely sprinkle on themselves and only a couple seconds played off as humor
There are multiple jokes in several episodes about attracive young girls, namely when the Todd performs a breast reduction on a 16 year old girl and shows remorse over the (waste).
One of the other staff members passes away, two separate family members to main characters pass away, and there are multiple instances of reoccurring patients eventually passing away.
Season 6, "My Cold Shower". In a fantasy sequence, Turk is imagining being married to Elliot--when she leaves for work, he cheats with their housekeeper (his wife Carla's role in the fantasy sequence)
There is an ongoing joke early in the show where they put a taxidermied dog in front of doors and such to surprise other people. It is mild but they try to cut the scene a bit jump scarey sometimes, with a scream and sudden zoom
There are episodes where people vomit but it is NEVER shown. It either happens offscreen or the person ducks away and make exaggerated puking sounds. The actual act is never shown.
There is an episode where a man is implied to be autistic (J.D number 1) has a joke with the main character (J.D number 2) and at one point J.D number 2 gets upset and yells at J.D number 1, Number 2 later apologizes.
A running gag involves JD's fantasy sequences, wherein he stares off into space and imagines strange and improbible situations. From time to time the show won't warn the viewer that a situation IS imaginary until we see JD "snap out of it", making for a minor dose of unreality.
JD says both tr*nny and tr*nssexual referring to trans women a few times in the show. One is played for laughs at the idea of Turk sleeping with a trans woman.
Several patients die starting in season one, most of them white.
Laverne, a supporting character and black woman, dies in season 6's "My Long Goodbye"--as it is season six, many deaths have preceded hers.
One Christmas episode sees the Christian Turk losing his faith after having to perform surgeries on so many people on Christmas Eve. He regains it later in the episode when something leads him to a pregnant patient in need, and he is able to save both mother and child
Sometimes women seen in their underwear, and it's not casual undressing ready for bed type, the way they strip is deliberate for viewers, plus some strong sexual references.