There are three scenes, from 2 movies, that stick with me decades after having seen them for the first time. They marked one of the few occasions in which mainstream SF films truly became art, as opposed to simply a narrative framework. And of course you find people who hate these scenes as often as you find people who love them.
Two are from Star Trek TMP: The shuttlepod flypast of the Enterprise, and the later sequence in which the Enterprise enters V'GER. I saw them on the big screen back when TMP first came out, and I have never no other film I've seen in the 30 years since have replicated the feeling I got watching these scenes unfold on the big screen.
The other is the psychedelic Beyond the Infinite sequence from 2001: A Space Odyssey, which I've been told is the closest filmmakers have gotten to accurately representing an acid trip on screen. I'm not into drugs so that aspect of it is lost on me, but it nonetheless took the film places where I didn't think a film could go. And I've only ever seen the film on TV and DVD; I can only imagine the big-screen experience.
Honorable mention: The closing sequence of The Quiet Earth.
Alex