Master of Magic: Civilization in a fantasy setting, and still has a loyal fan following over a decade after its release.
Duke Nukem 3D: An incredibly cool FPS back in its day. Too bad Duke Nukem Forever went vaporware AFAIK.
Kid Icarus: Everybody remembers Metroid, but few people remember this side-scrolling gem from the early days of the NES.
River City Ransom: Another little-known game that has a small but loyal fan following. This one was a
Double Dragon style beat-em-up with RPG elements and an incredibly addictive 2-player cooperative mode.
Crystalis: Anybody remember this one? It was a very cool Zelda-style adventure game for the NES, although with more RPG elements than Zelda had.
Defender of the Crown: I know that this one was actually remade not too long ago, but it failed to capture the coolness of the original.
Actraiser: One of my favorite SNES titles ever, with one of the most original premises I've ever seen in a game: You play as a god who has been slumbering for centuries to recover after losing a battle against a demon, and after awakening you set out to defeat your enemies and rebuild the world. Actraiser combined strategy, side-scrolling action, and one of the greatest video game soundtracks ever composed.
TIE Fighter: Best space combat sim ever. Not as story-heavy or character driven as Wing Commander, but
oh man did it have great gameplay! Plus, it gave you the guilty pleasure of getting to be the bad guy.
SimFarm: Following the success of SimCity, there were a deluge of "Sim" games released by Maxis during the 1990s. SimFarm was definately one of the best, and I actually ended up liking it more than SimCity.