Total SciFi have produced a list of the 100 best SF films ever. All in all a good list, with some obvious omissions and some questions over the order, but a great starting point to build your ultimate SF movie library.
Top 5 as per Total SciFi:
#1 Blade Runner
#2 2001: A Space Odyssey
#3 Star Wars
See the full list over at http://totalscifionline.com/features/3809