A few that haven't been mentioned as far as I can see:
Stranded (2001) was slightly similar to Europa Report (in style). I have to say I didn't like it, but it did show potential.
Apollo 18 (2011) had a premise which I found most interesting; the execution is mixed but their choice of aliens was (in my opinion) more creative than in Europa Report. For a sci-fi horror movie, I found this quite remarkable.
Dante 01 (2008) by Marc Caro (known for his work with Jean-Pierre Jeunet - Delicatessen, Alien: Resurrection) is a French style-over-substance movie with a considerable surreal touch. In terms of story there may not be anything groundbreaking, but it is clearly a (successful, in my opinion) visual experiment. I liked it a lot.
Moon 44 (1990, not so new admittedly), early piece by Roland Emmerich (Independence Day, 2012), a surprisingly well done and watchable sci-fi action movie rather typical of its time (or rather the 80s).
Monsters (2010), sci-fi in the sense of Peter Jackson's District 9 (2009), interesting concept but not really about science.
Primer (2004), Summer Time Machine Blues (2005) and Timecrimes (2007) as time travel movies - so technically science fiction but no spaceflight either. Very interesting though, in particular the latter two should not be missed, because they portray time travel in a very elaborate way.
Solaris (2002), not so unknown probably but not as known as could be expected from the cast: A free interpretation of Stanislaw Lem's novel rather than a remake of Tarkovsky's Solyaris (1972). Similarly to Dante 01, this is more an experiment in visual style than a story worth watching, interesting for a while at least, but not as much as Dante 01 (as I found). I found it rather tedious and boring to sit through, since most of the actual action and plot was stripped from the book.
Thanks for the Dante 01 recommendation, I didn't know Caro made a solo film and I'm a big fan of City of Lost Children, Delicatessen, and Alien Resurrection (Special Edition).