I didn't understand the reference to Naked Lunch until I saw the movie for the first time. Ever since then, that gag has been one of my favorite Simpsons jokes. Another great movie-related joke that went over my head until I saw the movie in question was this one from the episode when they go to Japan:

Marge: Homer, why are you so down about going to Japan? You liked Rashomon.
Homer: That's not how I remember it.