Eternal Sunshine of the Spotless Mind, definitely.

Howl's Moving Castle, Spirited Away, and Princess Mononoke were all very unique and different.

Moulin Rouge was very bizarre the first time I watched it, so I'd count that as a film that dared to be different.

Dogville is *definitely* a very very different sorta film. Almost like a stage play that someone decided to videotape. Didn't love the movie, but still, it broke out from the norm.

Brokeback Mountain. Gay cowboys. C'mon, that's pretty unique.

Hedwig and the Angry Inch. Very different. Very awesome.

There's soooo many more but I'm too lazy to list. Also, it's interesting that people though Crash was a different innovative film when I thought that what the movie did best was reinforce certain stereotypes.