It is tough, but I'd have to break it down by genre:
FPS: Doom: It's a classic, and 15 years later its still got a huge community pumping out mods and competing online, giving the game almost infinite replayability.
RPG: Fallout 2: I'm not a fan of RPG games, but Fallout 1 & 2 hit the spot. Fallout 2 gets recognition for surpassing its amazing predecessor, not an unheard of feat in video games, but when you consider the quality of FO1, its an impressive feat.
Adventure: Sam & Max Hit The Road: This game is the funniest game I have ever played. Seriously now what kind of logic must one have to attach Jesse James' severed hand to a broken golf ball retriever whilst holding a fish shaped magnet to jam it into the worlds largest ball of twine to get a psychic moodring for a swishy moleman living in a mystery vortex. No logic, is the answer. Plus, trying to say that sentence 5 times fast without taking a breath. I dare you.
RTS: TIE! StarCraft and Command & Conquer: Red Alert 2 Starcraft was an amazing title. By creating an interesting sci-fi universe and engaging story whilst giving us balanced and fun RTS gameplay, it succeeded in being one of the best. Red Alert 2 took everything its overblown predecessor had, and blew it up to even sillier heights. Silly, vibrant, insane, and ultimately fun was RA2's goal, and it succeeded.
I'll list more olater. Right now I'm tired.