1. Chrono Trigger (SNES) - well, it's the best game (IMHO of course).
2. Deus Ex - the best cyberpunk game on PC.
3. Well, I really don't know what to put there - Xenogears, Chrono Cross (any other good jRPG from Squaresoft?), some good RTS (like Total Annihilation). There are just to many good games (what about really old ones, like Tetris, Boulder Dash, Moon Patrol, Pong). Oh yeah, I know now what put here - Gyruss (Atari 800XL) - this game still rocks!

As much as I wanted to, I couldn't put them in any order. But here are my picks for Top 3 of All Time, just....in a chunk...
Final Fantasy Tactics - even modern games struggle to get the depth of this masterpiece's job class and battle customization. Not to mention a wonderful, almost too-complex story and beautiful character and level design.
Zombies Ate My Neighbors - just plain fun, unlike any game before or after it. It had the funny arsenal of weapons long before Ratchet and Clank (seriously, killing Mummies with tomatoes and kitchen plates never gets old) and addicting gameplay, what's more to like?
Indigo Prophecy - This is what art games should be. A story built for the ages (the ending was a bit "meh" I'll admit), but it had unique gameplay controls and extraordinarily cinematic editing and mise en scene. It felt like you were playing a Hitchcock flick.

Top 3 PC Games:
1) Civilization (all versions!)
2) Sensible World of Soccer
3) Championship Manager / Football Manager Series
Not a FPS in sight... :-)

Fallout 2, Giants: Citizen Kabuto and Planetside. Easily the top 3 of my favorite games of all time, but I honestly wouldn't put them in order from which I liked best in those top 3. They were all just as equally good.

1. Zelda Ocaraina of Time - Not going to explain this one because it's already been talked about to death
2. Shin Megami Tensei Nocturne - My favorite RPG for a number of reasons. The art isn't the same anime garbage you see in most jrpgs (see attachments below), the music is awesome (organ, guitars, demons screaming), The battle system is really deep and strategic without being overly complicated, way you form your party is similar to pokemon but with far more depth and consequence, And the story is amazing. Not many other games where you get to see the world destroyed in the first 15 minutes while you helplessly watch. After that you choose a philosophy around which to form the new world. A definite must for everyone who likes rpgs at all.
3. Zelda Majora's Mask - Made some strange changes to the structure established by Link to the Past, and is, in my opinion, as stronger game for it. This one's also been talked about quite a bit though so I won't waste any more of you're time.
I also want to give Diablo II, Persona 3, and Fallout honorable mentions.

Fallout, Fallout 2, not sure which I should post as third though...
If I go with time spent it should be Quake and QW (threewave CTF) online, with UT a close second. (CTF and online with that as well)
I'll have to add Duke Nukem 3D to the mix too, it was what made me play FPS's and got me to play more of Quake (which I didn't like at the time, until I tried it online and got hooked after seing the charm with FPS due to Duke)
Gothic was a pleasant surprise too though, I liked the gritty atmosphere and "living" NPC's and animals in it and then there's Chaser due to it being the best SP FPS I've played....
I'll go with Quake/QW CTF though, since I met some of the worlds best players in it and got a lot of excitement and got to know a lot of nice people through it.

Planescape: Torment - Awesome plot, and the gameplay was great as well.
Super Mario RPG: Legend of the Seven Stars - Really good game.
Baldur's Gate II: Shadows of Amn - Awesome CRPG

1. Duke Nukem 3D
2. Carmageddon
3. MechWarrior 2

StarCraft, Mass Effect and ... dunno... I guess maybe WoW? I spent alot of time playing it so it must have been good >.>
Or some classics like Starlancer, the Doom games, Half-Life (series)...

Fairly easy for me
PC
1) X-Com: UFO Defense. Still one of the best strategy games ever made.
2) Relentless: Little Big Adventure. The Temple of Bu is one of the more difficult platforming levels I remember growing up.
3) Final Fantasy VII. Listed here because I did not have a PS when this game was out and after enjoying it at my neighbor's house, I saw that CompUSA had it on sale right after release for PC for like $15 so I snatched it up. This would sell like crazy on GOG imho.
I realize this is about PC games, but because the Atari 2600 was a large part of my childhood I have to mention my three favorites for it as well.
1) Megamania
2) Raiders of the Lost Ark. Incredibly complex with the two joystick system
3) Taz

1. System Shock
2. Thief - The Dark Project
3. Little Big Adventure 2
I wish you'd just asked for the top two... those positions are well and truly fixed. I don't have a standard "third best game of all time", though, so you forced me to choose something! :)
I absolutely love the LBA games, and would probably pick the sequel over the original if I really had to, so I went with that.

Screw it, you're getting my top 10.
10) Pokemon Red/Blue
9) Half-Life 2
8) Conker's Bad Fur Day
7) Super Smash Bros.
6) Psychonauts
5) Final Fantasy IV (SNES)
4) The Legend of Zelda: A Link to the Past
3) StarFox 64
2) Banjo-Kazooie
1) Super Mario Bros.

1. Final Fantasy VI -- Greatest RPG of all time. The characters were great, the battle system was fun, and the twist in the middle of the game was epic...
2. Chrono Trigger -- A wonderful battle system and a fun, time-twisting story make this a close second to FFVI.
3. Portal -- A bit of a change of pace... This was short and incredibly sweet. The tricky puzzles alone would have made it great, but the addition of GlaDOS vaulted this to No. 3.
Honorable Mentions: Zelda: WInd Waker, Super Mario Galaxy, The World Ends With You, Starcraft

PC games:
1 - Doom2
It was awesome in it's day. and still holds up great now.
2 - Jedi Knight.
Half Life was awesome, but i had more fun with this.
3 - Deus Ex.
(or maybe System Shock 2 - since they are almost the same game).
Mentions to: Tie Fighter, Prince of Persia (original), Interstate76 and Terminator: Future Shock. & Portal.
Console:
1. Chrono Trigger (snes)
2. Ocarina of Time (n64)
3. Goldeneye (n64)
4. Sands of Time

fallout 2, half - life 2, fallout 1