This is a tricky one. I confess I struggled to think of a movie that I believe is great but is generally under-rated. In the end I have strayed slightly outside of genre. This is more of a comic book movie than pure science fiction, but I like the slow build as the plot and the twist reveal themselves. It is a film that gets over looked in discussions about M.Night Shymalan's deteriorating career. Bruce Willis and Samuel L Jackson are reliable as ever, as are the supporting cast. The script is good and the action sequences are almost shockingly real. In particular there is one fight with Willis's character just hanging on with a grim determination until his job is done. As a comic book fan I love the way that the raincoat Willis wears becomes a super-hero's cowl and cape.
I think Unbreakable is really under rated.