I second Zarch. For some reason I never liked virus. The control scheme was a lot better on Zarch, you could perform quicker movements and it had a better feeling. Virus seemed too loose and a bit spongey to me.
The pinball series was amazing. Dreams, Fantasies and Illusions all made some serious hours of fun. And to be honest no pinball game has ever come close. Especially not the one you get free with Windows.
I also second tomb raider. People forget that it came out on the Saturn first (some people forget it came out on the Saturn at all) but the Sony machine realised a good thing and bagged the exclusive rights for a while. Until that awful Dreamcast port was made. Dear oh dear what a poor conversion.
FFVII - Enough said about that one already. *cue highwind music*
I'd give a vote for Zelda on the Snes too. It was one of the best (and only) action-rpgs and frankly it kicked serious ass. It wasn't the first Zelda but it was certainly (IMO) the best.