Impossible question, does not compute, highly illogical, overload, overload, danger, warning Will Robinson, daisy... daisy... Just too many great and memorable sf films, many mentioned already.
One of favorites is The Arrival released in 1996. It reminds me of science fiction movie from the 50's. Very entertaining.
I'm committing heresy by not putting 2001 at the top of my list anymore, but I'm gravitating towards Contact, for its' passion, the extra unexpected possibilities in the narrative, and the frustrated yearning that is/should be common to all of us who empathize with the issues and challenges of daring to ask these questions in order to count ourselves as humans. And hey, points for a positive female role model, taking the high road at every impasse. With no screaming. If we can't have Carl back...can we at least have a real-life Dr. Arroway?
If I can only pick one... 12 Monkeys I love this film. It's everything a SciFi film should be, plus Madeline Stowe. Brad Pitt gives the performance of his career up to that point and Willis is a good cast for the role of time traveller James Cole; Terry Gilliam's best film, IMHO. Did I say I love this film?
I love Sci-Fi, especially those made in the 1950's. That said, my favorite would be Alien, which is simply an amazing movie.