Grim Fandango. I just love the world.

Soul Reaver.

The game has a strong atmosphere, with an interesting gameplay mechanic where you can move between the underworld and the overworld. In the underworld, the geometry of everything twists and warps and different enemies spawn, which adds another dimension to the puzzle elements of the game.

The world building, atmosphere, voice acting, music, puzzles, and combat are all great for the time.

There's an upscaled version of the opening cinematic here to get a feel for it: https://www.youtube.com/watch?v=tkkmm9vqbHQ

Ocarina of Time, hands down.

Quake.

It set the stage for many a truly 3D Person Shooter. Plus, the atmosphere, the motif. Dark Gothic game with Sci-fi and Eldtrich horror elements.

The pace is always breathtaking and it's just perfect for me. Action, suspense, and sometimes just looking around in the moments where you have time to spare.

That's a tough one.
In terms of graphics and general vibe, Unreal, hands down.
When it comes to gameplay, I'm leaning towards either Soul Reaver or OOT, which I see other people here have already mentioned. I also quite like San Fransisco Rush 2049, even though I only find it enjoyable in short bursts.

Half-Life as it's one of the first PC games I ever played and I still play it to this day. Plus, the speedruns are very enjoyable to watch, and it probably has the best bunny-hopping out of any video game in my opinion.

I guess since Perfect Dark was technically in 2000, I'll say Donkey Kong 64. That game blew my mind when I was 11.