I'm not going to make an ordered list.
Shadow of the Colossus is pretty much my definition of a perfect game, excellent atmosphere, EPIC gameplay. Half-Life (not 2) is also pretty high up there. DooM (and DooM 2) is amazing, and still holds up to this day, and on the same note, Duke 3D. Blockland is definitely one of my favorites, even though I can't build for ice cream. Pretty much any 2D Worms game, with the exception of Open Warfare 1 on the DS, because of the amazing gameplay and multiplayer. Timesplitters 2 is, in my opinion, the best console fps ever. Psychonauts, for being an ingeniously funny platformer, and The Milkman Conspiracy. The two PS2 Katamari games are near and dear to my heart, too. I absolutely adore LocoRoco. Sven Co-Op is probably my favorite mod ever. One of my favorite RPGs is Mario and Luigi: Superstar Saga on the GBA, it's hilarious, and it makes turn-based battles fun. MarioKart DS is probaly my favorite racing game, or DS game. Pokemon Yellow, oh how I regret trading you in. The Incredible Machine 3, for being my first physics-game ever, and still being awesome. Portal, for making me laugh and think, while providing amazing gameplay. Elite, the most amazing space sim ever. The Legend of Zelda: Links Awakening or The Legend of Zelda: A Link to the Past are my favorite Zelda games. I'd have to say Super Metroid is my favorite 16bit game, with Chrono Trigger being a close second. Ducktales, because it has the most pandaing awesome music ever. Super Mario Galaxy made my jaw drop a few times, in a good way, and is probably my favorite Mario platformer. I played the heck out of the first Star Wars Battlefront, and the sequels just don't hold up to the first. Beyond Good and Evil did 3D Zelda-style gameplay better than the 3D Zelda games. SimAnt, because it's so simple, yet so fun. Noctis, as it's the game that got me into freeware, and also how I made friends with Aloshi. WarioWare Inc. MEGA MICROGAME$ is an amazing GBA game. Yoshi's Island on the SNES is my favorite 2D Mario platformer. Tetris DS, my favorite Tetris variant. Burnout 3, my favorite racing game. Star Control 2, the OTHER best space game. Tie Fighter, the best Star Wars game. Nethack, the most awesome dungeon crawler ever. Pretty much any Harvest Moon game, the core mechanics are soo addicting. Knytt, my favorite Nifflas game, with Knytt Stories (I'm in the credits :P) as a close second. Lyle in Cube Sector, an awesome free Metroid homage. Scorched Earth, THE MOTHER OF ALL GAMES. Hover. Super Mario Land, for that hella awesome music. Kirby's Adventure, on the NES, one of the first games I ever beat. Driver, even though I never got past the training mission, making movies of epic chases was (and is) sooo damn fun. Armadillo Run, because it's like TIM with awesome physics. Team Fortress 2, the greatest multiplayer fps in recent memory. Spheres of Chaos, because it's Asteroids, but TRIPPIN' BAWLS. And some more that I can't remember. By the way, this is my longest post ever, and the one I'm the most proud of. I'll add more as I remember.
EDIT:
OH MY GOD I FORGOT PLANESCAPE TORMENT.