No particular order:
Final Fantasy 6: To me, the last, great JRPG. It had a big cast of great characters, an epic story with a big twist, its cutesy character was actually fairly badass, and the music is still legendary. (See: Opera scene.) I'll allow that FF7 was pretty awesome, too, but then it became the model for every single Japanese RPG after it, and totally mauled the whole genre. Stupid FF7.
Mass Effect 2: Generally speaking, there's at least a 2-3 year waiting period before a game can be placed on my Top X Games list. But Mass Effect 2 is just that phenomenal. Such a great game.
Knights of the Old Republic 2: I know, I know. KoToR1 was the classic, and KoToR2 was unfinished and its storyline was a mess (those two facts being very closely related). However, it painted the galaxy less in shades of gray rather than the first game's stark black and white, made you a Jedi from the start, began with a tense showcase of roughly what an HK model can do without your guidance, dealt with themes of redemption, corruption, and the battle of cynicism vs. idealism, had the really interesting philosophies of Kreya, had much more thought-provoking conversations with HK-47, and didn't have Carth Onasi. (Well, beyond a couple of cameos.)
Baldur's Gate 2: Minsc. Boo. Irenecus. The Underdark. Player strongholds. Involving sidequests. A truly epic feel. BG2 is the epitome of classic RPG game design, and you need to play it if you haven't.
Quake: Probably an odd one, but I sank way, way too many hours of my high school years into this game and its hundreds of mods. It was my first FPS, it was dark and intense, it was filled with cool monsters, and people were crafting new maps and games out of it constantly. Some of my fondest gaming memories are of Quake and the original Team Fortress. (And so are some of my frustrations...friggin' snipers with OpenGL cards and their transparent water!)