[RustedCorpse]

In Eternal Sunshine of the Spotless Mind there are a ton of scene's very early on where Kirstin Dunst and the Doctor (forgot actor) have some intimate background moments. At one point he places his hand on her should and she just stares at it with this longing. It's hilarous.

In Donnie Dark, there is a halloween scene and someone dressed as Regan is jumping on a trampoline, ala Hunter S.

Edit: In Barton fink there are so many references to hell. In the elevator they mention the number six three times. Plus whenever Goodman/Satan is around is the only time the room sweats and peels.
In Stay (which anyone enjoying subtle, trippy movies should watch) there are TONS of background nuances. People are reused in every crowd scene. Hamlet quotes abound, and the Hamlet play scene is a pretty powerfully subtle statement.

Rules of Attraction: When Sean answer's Paul's phone call and says "Patrick?" I busted up. (His older brother is Patrick Bateman)

Also in Lebowski, The Dude never actually bowls.