I have recently watched a film called “The Fountain”, written by Darren Aronofsky, a very spiritual metaphysical movie of life, love and death (kind of like “The tree of Life” but with complete constructed dialogue that makes sense). The movie tells a story over three time periods which are all interlinked.
It might be too high-profile to be a hidden gem (although it didn't do very well at the box office) but the recent
Cloud Atlas film did remind me a bit of
The Fountain and although it wasn't as good as the book I still think it was a good film.
Some other good non-Hollywood SF/Fantasy movies:
Cube - it was a very tense and claustrophobic film and very effective for something that was probably made on a tiny budget. The sequel was a bit rubbish, though.
Avalon - a Polish language live-action film by a Japanese animé director (this is almost certainly the only film that could be described in this way) about a woman trying to making a living in a virtual world.
eXistenZ - another virtual reality film this time by David Cronenberg, it was a strange and very memorable film. Might actually be a Hollywood film, but doesn't feel like one.
Brotherhood of the Wolf - perhaps technically not a fantasy movie but it's not far off. You won't find a better French language historical fiction/martial arts/based on a true story/monster movie.
City of Lost Children - the director is more famous for
Amelie (and infamous for a certain Alien sequel) but I think this is his best film.
Intacto - a Spanish film about people with the ability to absorb other's luck competing to become the luckiest person in the world. Very rarely mentioned, but I liked it a lot.
You've reminded me that I have the DVD of
Eden Log but haven't watched it yet, it does sound potentially interesting.