Chrono Trigger, for me, is the best RPG ever.
The reason I can't name new games as the best, is because they're not inventive. The NES, SNES, Commodore 64 games and the like are the ones that made a genre, they were the benchmark. Most of them still are.
Sensible Soccer, the game made 8 years ago, still has the biggest accurate database of any football game.
Chrono Trigger is still the world's most innovative RPG - alongside the first Zelda game on the NES.
Why has barely anyone mentioned Doom? The game that made the FPS games what they are today? And if not Doom, then Goldeneye at least - the best multiplayer FPS made.
I'm going to save myself the time of mocking all the people naming very new games, such as GTA's etc, and assume they are too young to play the old ones.
EDIT
Should probably add Championship Manager 97-98 here. The Championship Manager games are the only new-generation games I genuinely believe are class. And even these are getting less appealing. I still play CM 01-02 and am still very addicted, but CM4 offers me nothing new.
Golden Axe was a classic game, it was the first two-player co-operative game I played where I really felt there was team-work involved. It was the game that introduced me to multi-player gaming.
I s'pose, at a long-shot, you could make a case for the Breath of Fire games, Super Mario World is the best platformer made, and there was also a game called History Line - on the Amiga I believe - which I found simply amazing at the time.