A true classic, if not as well known as some of the other titles on here. Hostile Waters is a slick blend of action and strategy that is immensely playable and a hell of a lot of fun. It's a bit slow to start, but give it a few missions and you'll come to love it. If it had feature multiplayer, I bet it would still be played today.
And for geek bonus points, it's narrated by Tom Baker (Dr Who) and Avon from Blake's 7.