This is tough. I was still very young and already loved sci-fi movies and tv when I started learning how they were made, and that just made me love them more.
In order of release date rather than preference, because the latter would just be too difficult:
Forbidden Planet (1956)
I first saw this at a very impressionable age, and that monster lived in my head for a long time. This is an amazing piece of '50s scifi. MGM famously spared no expense in making it, and it shows.
When we first meet her, Altaira is a great character, despite being treated pretty horribly by the men around her, but she eventually gets relegated to mere romantic interest.
It doesn't hurt that this is a very loose adaptation of The Tempest, one of my favorite Shakespeare plays.
It also doesn't hurt that this feels almost completely like an original Star Trek episode, which I already loved by the time I first saw this.
2001: A Space Odyssey (1968)
I saw this when I was too young to even remotely understand it, but even then it had a hypnotic effect on me. It's still a very meditative movie for me. I get why many people find it too boring to sit through, but for me the combination of the pacing and the artistry is really immersive.
Star Wars (1977)
I mean, come on.
I saw this 7 times in 1977, and most of those involved riding my bike for miles each way. I don't know how I managed to have the money for a ticket 7 times.
I think I was just the right age for this when I first saw it, so whenever I rewatch it I still vividly remember how it made me feel that first time, which connects me to a younger version of myself.
Star Trek II: The Wrath of Kahn (1982)
I had been a bonafide Trekkie since the omnipresent '70s reruns. I loved The Motion Picture, and still love it, despite being aware of it's flaws even at my young age at the time.
TWOK has taut storytelling, a strong narrative spine, well-written characters whose actions come from real places, some great performances, a fantastic score, and a truckload of great moments.
I don't know how many times I saw this in it's first run, but I saw it 12 times at a second-run theater.
Arrival (2016)
Some of Denis Villeneuve work has a similar effect on me as 2001, above. I love truly alien aliens, and I will watch Amy Adams in anything. I love the storytelling layering in this and how the ending almost explains it.
Honorable Mentions:
The Day the Earth Stood Still (1951)
A stone-cold classic. There's a lot of innovation in this movie, and it does so many things so well.
What does it say that Robert Wise directed three of my favorite movies: this, Star Trek:The Motion Picture and West Side Story?
Planet of the Apes (1968)
It really hurts to not have this in my top 5, but choices had to be made.
Bladerunner (1982)
This has dropped since my most recent viewing a few years ago, because how Decker treats Rachel is pretty vile.
I had Gravity (2013) on this list, but it's a science fiction movie only in the sense that it's fiction and there's a lot of science and technology in it. It's more of a tech thriller, really. But "astronauts in trouble" is one of my favorite (sub)genres, so...
So, that's almost my top ten right there!