There's one in the theater right now that you guys NEED to go see: Peter Pan. It's not unknown, but it's being ignored, and it's fantastic in both senses of the word. Don't expect a retelling of the cartoon version: this one hews close to the theatrical version, with a murderous Tink, a Captain Hook played by the same actor who plays the father, and realistic but unsettling sensuality in the two preteen leads. The effects are close to Baron Munchausen in aesthetic. Good stuff!
Okay, other movies, not complete unknowns but still a little obscure:
The 5,000 Fingers of Dr. T is great, as someone already mentioned. Live action ubertrippy Dr. Seuss movie, with the creepiest dance duel ever filmed.
The Vanishing, a French horror movie that's scared me more than any other movie I've seen. From what I've heard, stay far away from the American remake.
Living in Oblivion, an unheard-of arthouse flick about making an unheard-of arthouse flick. Steve Buscemi is always fun, and it's got the funniest dwarf scene evar. Although it starts slow, few movies have made me laugh as hard as this one did.
Daniel