Hi All,
There have been lots of very good and excellent ones mentioned already -- but really, in the end there is no contest:
Years, if not decades ahead of its time in special effects, direction, sound-track, camera-work and overall execution is ...
"Open the pod-bay doors HAL"
... (2001 A Space Odessey).
The attention to detail on the physics, science and astronomy is exceptionally high considering it was made in the mid-60s.
Leaving aside the genre, it is widely considered one of the best films ever made full stop
http://en.wikipedia.org/wiki/2001:_A..._Odyssey_(film)
Honourable mentions go to all the Star Wars films, Contact, Forbidden Planet and Apollo 13 (more a docu-drama than Sci-fi but ...)
Best,
Les D