Zelda: Wind Waker
Personally, I liked this game the most. It was a non-traditional approach to the series, yet it created a game that felt like a Legend Of Zelda game should. It's you vs. the world, on an adventure in uncharted lands, plenty of mystery, plenty of side quests, exciting combat, satisfying puzzles, everything it should be.
It felt like and adventure, and it was fun and exciting. It's how it should feel. And the visual style was beautiful. The graphics, much like TF2, will never age.
Bit.Trip: Runner
Runner was a fantastic entry in the Bit.Trip series, and it was so satisfying and challenging to power your way through each level, the music becoming more detailed and euphoric the better you did. It was just pure fun.
Animal Crossing: Wild World
Wild World improved on the Gamecube version in almost every way, added loads of new content, and was incredibly addictive. Plus, it was portable. I think City Folk took the wrong direction by putting the hidden stuff into the city. Everything was just...there. But this game felt fresh and new.
Ratchet and Clank: Up Your Arsenal
I didn't play the PS3 Ratchet and Clanks, but I had the most fun with this one. It solidified the mechanics of the past two and gave it a better story and more polished feel. I really liked it.
Sly Cooper: Honor Among Thieves
The strongest narrative wise of the series, and a good example of how to make new mechanics like vehicle stages actually feel right.