I would have to say that Blade Runner is probably the best Sci-Fi film of all time, on so many levels. It has it's share of action, but it is also very thought provoking too.
Serenity is an awesome film. The dialog is sharp and witty, and admittedly, a more than passing familiarity with the series does make the film more interesting, you can certainly watch it on its own.
As a personal top 5:
- Blade Runner
- Star Wars: A New Hope
- 2001
- Terminator 2
- The Abyss
Honourable mentions for: The Running Man, Total Recall and Predator.
I also think that Waterworld is a vastly underated movie.