Contact The Adjustment Bureau 12 Monkeys The Terminator The Abyss AI Artificial Intelligence The Day The Earth Stood Still War of the Worlds (1953) Minority Report Wall-E Ex-Machina Source Code Ender's Game Star Wars IV: A New Hope
I really enjoyed the original Star Wars films, The Fifth Element, The Matrix, Gattaca, Starship Troopers, and I also enjoyed the new Dune films (albeit, think they would have benefited from some editing...).
Perhaps more tenuously sci-fi, I also liked S1M0NE, Tremors (1-3), Chronicle, Mad Max Fury Road, and Inception.
Also while not strictly "good" films in some senses, I did enjoy in their own way Aeon Flux, Galaxy Quest, and I, Robot.
Note sure if they count as sci-fi at all but I also liked the old Toho Godzilla films when I was a kid