Super Mario Galaxy - Blew me away in a way few games did before and none have ever since.
Skies of Arcadia - Started off as a fun RPG but when Vyse got stuck on the island and had to find a way to leave, at that point the game clicked with me and became a classic. Gorgeous environments, memorable music, I was legitimately sad when I beat the game. It was such a pleasant surprise to see a Skies of Arcadia getting repped in the latest Sonic racing game.
Super Mario World - Loved the music, loved the way they evolved the formula of the game, and it confuses me when people say SMB3 is better. SMW is such a better game in almost every way.
These are probably my permanent top 3. The other two games would include but not limited to: Goldeneye 007, Super Mario Galaxy 2, Red Faction Guerrilla, Borderlands 2, Banjo Kazooie, Final Fantasy VI, Grandia 2, Super Mario Bros. 3, Warriors Orochi 3, and Dynasty Warriors 5.