To this day, I still have no idea why people always say Donnie Darko is one of the best science fiction movies. It's watchable, but barely. I think it happened when a bunch of trendy hipsters decided they wanted to pick a B-movie to claim was awesome, and then from then on out everyone wanted to be cool and join in on saying it was the best movie they'd ever seen. It was subpar, to say the least; I'd rather watch Eraserhead.
I am with others on Paycheck and The Butterfly Effect (haven't seen any of it's sequels). I liked Next from what I saw of it (about half). Dark City is not bad and definitely has a pretty good premise, but I think it will have to get re-made in the future because I don't think it was done as well as it should have been.
I'll toss one up that's come out recently, but that I think a lot of people haven't seen: Moon. It's not action-based like most of the others mentioned, but it's definitely one of the better Sci-Fi psychological/drama movies I've seen in a while.
If you're looking for one with a little more action, Pandorum is pretty good.
And yes, I'm ignoring the whole time-travel idea/future prediction idea and going more with the overall messages / feels of the movies