I ran into this list of the greatest science-fiction films of the decade, composed by the folks at Sci-Fi Squad, and I found it generally well thought-out and hard to argue with with a few exceptions.
Children of Men, Minority Report, Donnie Darko are no-brainers, musts, but the exclusion of Danny Boyle's Sunshine irks me a little, especially in favor of stuff like Serenity and Timecrimes.
Now everyone and their neighbor knows that Sunshine kind of veers a little off-course in its final act, but it's still a slickly-produced, well-founded and sporadically brilliant end-of-the-world space mission. Plus John Murphy's original score is easily one of the most ingenious, copied, and repeated compositions of the decade - topping his 28 Days Later work.
I can't think of any other potentially worthy sci-fi stuff from the '00-'09 period, any other notable omissions? The list:
Children of Men
Eternal Sunshine of the Spotless Mind