Blade Runner - Final Cut (followed by the Director's Cut). I think it may depend on which version you've seen first and what kind of movies you're into in general. As I prefer Japanese movies, I like neither the over-explanation nor the artificial atmosphere of voice-over narration. Plus, the happiest ending of my 10 favourite movies is from A Clockwork Orange and the fact that Blade Runner's happy end is just stock footage from Shining doesn't make it any better.
Apocalypse Now - Theatrical Cut. Redux has so many unnecessary added scenes of lower quality than the rest movie that Kurtz' Compound just seems like another unimportant stage of the never-ending journey. And I hate the exotic 2:1 aspect ratio.
Alien - Theatrical Cut. I also hate the cocoon scene because it's overly complicated for the first movie and doesn't make any sense without a queen (and even less after the activation of the self-destruct).
Aliens - Haven't seen the Director's Cut yet.
Terminator 2 - Haven't seen the Director's Cut yet.