I love the scene near the end of The Royal Tenenbaums in which Chas is violently attacking Eli and throws him over the backyard wall; he follows him over and both end up lying peacefully in the zen garden next door.
Also from The Royal Tenenbaums, Margot's line, "I can't even begin to think about knowing how to answer that question."
In Superbad my friend and I seemed to be the only ones who laughed at a particular scene, but I thought it was the funniest in the movie: The two cops are talking to McLovin in their squad car, and quote something from Star Wars. They say something to the effect of, "That's Yoda, you know, from Attack of the Clones." I got a kick out of that.
From Paper Moon, Addie anouncing to the policeman that she has to go to the "shithouse."