I think the montage of bad US foreign policy acts set to Louis Armstrong’s “It’s a Wonderful World” takes the cake for me. Even though I’ve seen the movie about 10 times, once the music stops and they show the second plane hitting the WTC, I still get misty-eyed.
Another scene in Vanilla Sky has Tom Cruise freaking out and screaming while “Good Vibrations” by the Beach Boys plays. I thought that was a really unnerving scene.
I saw the movie, but don’t recall that scene. I do recall, though, that in the book Howard W. Campbell (Bolte’s character) has something like 19 copies of that record.
Additional examples:
The bar fight in Mean Streets, set to some upbeat Motown girl group.
The napalming in Good Morning Vietnam is set (as were a few other examples mentioned here) to Louis Armstrong singing “What a Wonderful World.”
This isn’t cheery music, but I’m reminded of the family scene in Natural Born Killers with Juliette Lewis and Rodney Dangerfield as her foul-mouthed, violent, drunken father, which is shot like a sitcom with cheery graphics and a laugh track.