The Last Starfighter was great, and had the best sci-fi villain of all time:
Also, Masters of the Universe. Movie might have been cheese overall, but movie Skeletor was an amazing villain, perfectly acted as well, and blew away his moronic comic book counterpart.
And then there's Dune... a movie that broke with some of the book lore quite significantly, but still managed to remain true to it - and happened to spawn one of my all-time favourite games. One might even consider Krull sci-fi.