MirrorMask.
Neil Gaiman + Dave McKean + Jim Henson Company = Beautiful CGI, a compelling story, original ideas that really shine. Plus, it's incredibly well acted.
It's hard to say what really is obscure though. As I'm sure this wasn't intentionally as small as it became (and to be honest, I have no idea how popular this movie was).
Memorable mentions are Saved! with Mandy Moore (genius comedy) and Final Fantasy: The Spirits Within (I thought it was a wonderful Sci-Fi movie, and I do consider this obscure as a lot of the gaming community knows about it, but outside of that it's just not remembered at all) and finally Shortbus (the porno with a heart or the movie about sex that doesn't shy away from real sex scenes, call it what you want).