Well, I can admit I'll probably forget a few from the latter half of the decade; I started really enjoying gaming with Crash Bandicoot 3 (which means that two thirds of the N-Sane Trilogy will be brand new to me :D ), so I'll do what I can. These are in some particular order, but I haven't played some in like 20 years:
Half-Life
Riven
Myst
Quake
Doom
Crash 3
Banjo-Kazooie
Banjo-Tooie
Spyro 2
Ape Escape
I think that's about every game I even remember from that era, at least that I played and really enjoyed.
You?
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GoldenEye Pokemon Gold Super Mario 64 Banjo Kazooie