This list will be skewed towards console games since I have never owned a decent gaming computer (and I recognize that games like Half-Life 2 or something could possibly make the list). Also, no particular order:
1. FFVII (PS1) - Still the greatest Japanese-style RPG ever made. Everybody's still trying to catch up to this one.
2. Metroid Prime (GC)- One of the top 3 current-gen console releases
3. Super Mario 64 (N64 - I believe this game to still be the best example of utilizing 3-dimensions thus far
4. Legend of Zelda: A Link to the Past (SNES) - One of the first SNES games released; arguably the best 2d game ever.
5. Super Metroid (SNES): Probably the only contender against #4. One of the earlier examples of atmospheric narrative.
6. Halo (Xbox): A shooter with a kind of spatial complexity that had never been seen before.
7. Legend of Zelda: Ocarina of Time (N64) - No words are needed.
8. Castlevania: Symphony of the Night (PS1) - One of the best soundtracks ever; borrows from the masterful Super Metroid. Throw in some original stuff and you got a masterpiece, another awesome 2d game.
9. Final Fantasy Tactics (PS1) - Awesome gameplay with an intriguing story. The story resonates in its presentation through ideas, gestures and music and not the actual content.
10. Super Mario World (SNES) - To me, this is a better game than Super Mario Bros. 3. This has such a purity and sharpness in its design.
Here are the runner-ups, those that have the potential to be top 10 on some other days when I'm making a top list:
Ico, Shadow of the Colossus, Metal Gear Solid, Brothers in Arms 2, Final Fantasy 3/6, Chrono Trigger, Xenogears, Earthbound, Mega Man X, Mega Man X2, Super Mario RPG, Sonic the Hedgehog, Gain Ground,
all Silent Hill games,Legend of Zelda, Contra 3, F-Zero, Resident Evil 2, Half-Life 2, Halo 2, Sonic Adventure and probably a lot more I'm forgetting at the moment.