A lot of good games came out in the late 90's that have had a profound impact on today's games:
Daggerfall (Elder Scrolls)
Command & Conquer (Real time strategy forerunner)
Starcraft (Again, real time strategy, but better)
Thief (the original, games like Splinter Cell series, stealth combat)
System Shock 2 (The Bioshock series and countless other 1st person RPGs)
Everquest (The first 1st person view MMO, spawning many others including WoW)
Anarchy Online (technically 2000 I believe, one of the first futuristic/space MMOS)
These are just a few I played , but I am sure there are many others people remember.