I'd say Serenity.
Also a fan of SF will probably like The Prestige, because (a) it's good, and (b) it deals with some SF concepts, albeit not in a conventional SF style. It mentions people like Edison and Tesla, for example, and some of the things Tesla is credited with amount to science fiction. It's by Chris Nolan; I'd say his earlier film Momento would also appeal to SF fans; which may give you an idea of where I'm coming from.
Contact is one of the few real SF films of the last 15 years, but it's just outside your time interval.
There's a lot of Horror that can be SF-like. Silent Hill, for example. Some people have Pan's Labyrinth down as fantasy, but that's a matter of interpretation.