2001: A Space Odyssey -- had a profound effect on me as a child. It both reinforced my interest in science and opened my mind to the sheer size and scale and mystery of the universe. The original Cosmos series did likewise, and I think it's far better than the remake with Tyson. Sagan just communicates the sense of awe and wonder a lot better.
Wargames -- definitely made an impression on my pre-teen self and helped get me into "hacking" (sense #2), which led here through a long and winding road.
Stand By Me -- a profound film about the end of childhood. (The Stephen King novella 'The Body' is good too, probably almost his best work.)
Primer -- the best sci-fi of the past decade. When you don't have a big budget to plaster FX all over the screen, it's got to be in the writing. Big budgets do sometimes ruin cinema.
Enter the Void -- this is a weird recent one that stuck with me. This is definitely a binary reaction film. I loved it, others hate it. It communicated the profound sense of loss that comes when you're forced to leave a thing unfinished and move on, followed by the sense of hope that comes with a new beginning. It was also just the visual aesthetic of that film. It haunts me. The artistic ethos of this film felt as if someone lifted dreams directly from my soul and rendered them on screen. Night flights over neon cities is probably what I'll dream about as I die.