Well, on top of my head:
Popol Vuh's for Aguirre and Nosferatu, Ry Cooder's for Paris Texas, Neil Young for Dead Man, Danny Zeitlin for The Invasion of the Body Snatchers, Cliff Martinez's for Sex, Lies, and Videotape, and Michael Brook's for Affliction. Lalo Schiffrin used to put out amazing soundtracks as well.