Prince of Persia The Sands of Time.
Its got the best platforming that I've ever seen in game. In fact, to put it bluntly, Sands of Times platforming is unmatched by any other game I have ever played, end of. Its also got two of the most believable characters I've ever seen in a game AND it's about the only game ever thats got romance right. What else can I say? The puzzles where genius, graphics where surprisingly good, the story as a whole was great (its one of the few games I've played that is almost better in the retelling) and its one of the few games I've ever played thats brought me close to tears.
Truly a master piece of a game.
EDIT: While PoP SoT is currently my favourite my opinion changes weekly, so heres my top 5.
1.Prince of Persia: The Sands of Time
2.Portal
3.Psychonauts
4.Team Fortress 2
5.Shadow of the Colossus