An edited version of "How To Be a Werewolf" on the new Mogwai album was used in some kind of short film...pretty awesome too. I could see Mono's "Follow the Map" in an Anime film hahaha.
Honestly though, check out Sigur Ros' (), the ambient side of Rosetta's The Galilean Satellites and The Cleansing Undertones of Wake/Lift, and Lights Out Asia's In the Days of Jupiter.