Hmm. Most people would probably expect me to say either Starcraft or Fire Emblem 10 (or, to those with good memories, FE7). Most people, however, are wrong. Those two are definitely up there, along with KotOR, Mutant League Football, FFVI, VII, and Tactics, Deus Ex, No More Heroes, Shining Force 2, General Chaos, Metroid Prime 3, and Civilization 3.
But in the end, I'm still with The Legend of Zelda: The Wind Waker. So much smoother than previous 3D Zeldas, not to mention the timeless graphics and holyshitthisisawesome final boss fight.