Honourable mention to Event Horizon, which is the only film to *really* have spooked the hell out of me. But that's really a horror film - the sci-fi aspect is just the scenery.
Honourable mention to Forbidden Planet. The visual FX still hold up pretty well, even today.
Honourable mention to Terminator. Unfortunately the digital FX on Terminator look fake these days - the scene with the metal terminator charging for the door is completely unconvincing now.
And final honourable mention to Dune. Shame it was so badly hamstrung by budget cuts, and shame they added the rubbish "weirding modules" for no particular reason. But up to Paul Atreides reaching the Fremen, it was nearly perfect.