1. The Legend of Zelda: Ocarina of Time (Skyward Sword, in my eyes, took the title for best Zelda game, but ocarina of time was more influential and still stands the test of time.)
2. Star Wars: Knights of the Old Republic (The sequel and the MMO are good, but this one set a new standard for western RPGs and licensed universe games.)
3. Super Mario Galaxy (While the original Super Mario Bros. probably deserves the top spot, I find myself going back to Galaxy more than any other. The art style, the music and the unique game play make it an experience more memorable than most games of the last generation.
Honorable Mention: Metroid Prime (I know that most Metroid fans would rank Super Metroid over Prime, but Retro's reinvention of the series into 3D really was a masterpiece.)