According to James Snyder of Techland:

5. Silent Running

4. Gattaca

3. Serenity

2. Dark City

1. Primer

Link with film!

Do you have any others?

My favorite though Sci Fi movie that wasn't big in the US would be 2046, which grossed a little over a million dollars (not bad though for a foreign language movie), which I am so happy I saw in the theater. Sad, beautiful, complex— a movie about the nature of existence while also being chic.