My all-time favorite movie pun is when the nerd on the deepsea drilling platform in The Abyss reveals that Navy SEALS have secretly brought aboard a nuclear-warheads package, announcing, “Heeeeeere’s MIRV!”
In The Shining, a distraught, knife-weilding Wendy happens across someone in a weird sort of bunny suit getting it on with some dude on a bed.
When Jack goes “Honey, I’m home” after opening the axed-up bathroom door.
In Rosemary’s Baby, this pleasant exchange:
Rosemary: What have you done to him? What have you done to his eyes, you maniacs!
Roman Castevet: He has his father’s eyes.
The little boy sees that, not Wendy, I believe.
No it’s Wendy that sees it, and it’s two of the hotel ghosts, one of them is doing that “furry” fetish thing:
But given the context of the OP, I don’t consider this to be a funny joke.
I gather (correct me if I wrong) that you see it as more of a surreal than humorous thing.
As per the OP, it’s definitely a dark movie, and I guess we can debate if it’s the funniest thing in the film (“Heeeeeeere’s Johnny!” - nah).
A bit of dark humour in the scene where Jack rails about being disturbed while typing, and Wendy later on coming across the “All work and no play makes Jack a dull boy” papers. (well, eliciting a sort of :eek:-type laughter anyways)
In the somewhat eye-opening final dinner scene in The Cook, The Thief, His Wife and Her Lover, Helen Mirren holds her rotter of a husband at gunpoint to get him to eat her just-cooked lover, advising, “Try the cock, Albert. It’s a delicacy. And you know where it’s been.”
Ah, thanks. I’d misremembered that.
Pulp Fiction - “let’s not start suckin’ each others dicks just yet”
Going a bit off topic, I have no idea why Kubrick left this scene in the movie. In the novel there’s a whole backstory about gangsters who used to stay at the hotel in the 1930s and about how one of them was gay and into the furry fetish thing, and if I remember correctly was murdered in the hotel. The backstory completely explains the ghosts Wendy sees. Kubrick cut out that whole backstory, but left in the scene where Wendy sees the ghosts in the middle of a sex act. Without the backstory that scene doesn’t really make sense to the audience.
Malcolm X. Malcolm Little’s street name was Detroit Red, because he used a relaxing agent that gave his hair a reddish tint. It was established early that he had to rinse it out at precisely the right time or it would burn his scalp. The second time he’s seen using it, he’s about to rinse out when he discovers that the water has been shut off in his apartment… at the same time that there’s a lot of pounding on the door. “Police! Open up!” No shower. No sink. Uh…And that’s how the cops find him: with his head in the toilet.
Also, when he’s in prison and converts to Islam, he writes to Shorty, Spike Lee’s character. Voiceover of Malcolm gushing about Islam and Allah, and Shorty shakes his head. “He’s gone nuts.”
My guess is for shock value, since Wendy’s slowly realizing at that point that her husband has been taken over by the spirits in the hotel. But hey, some Dopers thought it was funny, so maybe Kubrick had a twisted sense of humor? 
“Dark” has very little humor. But there’s a little moment set in 1986 at the asylum. A prisoner who’s been there for 33 years is nicknamed “Der Commissar.” So as one of the guards goes by, he jokes, “Alles Klar, Herr Commissar?”
Supernatural - Dean Winchester, “Dad would’ve loved this thing!”