1. Blinx: The Time Sweeper - If you don't know this, then you clearly don't know me well enough
2. Pikmin 2 - A very close second, I found the strategy when playing the game really fun, and it's pretty easy for beginners to pick up
3. Sonic Adventure 2 - So many features that were done right. Near flawless controls, fair difficulty, Chao garden, good story, and great level design.
4. Monster Tale - One of the most obscure games I know. Normally they are either really bad or really good. It's a lot like 2D Metroid and Pokemon.
5. Pokemon Mystery Dungeon 2 - The first pokemon game where they put more than 10 seconds of thought in the story. One of only two games that made me cry, the other being Mother 3 (for obvious reasons).
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Honorable Mentions (not in order):
Spongebob Squarepants: Battle for Bikini Bottom - Best licensed game I've ever played. One of my all time favorite platformers.
No More Heroes 2: Desperate Struggles - Controls well, loved all but 3 bosses (Million Gunman, New Destroyman, Matt Helms) and a pretty good message near the end.
The Munchables - Another obscure gem. Think of it like Katamari Damacy except with combat and bosses.
Banjo-Kazooie - Another great platformer, the game's humor, music and gameplay make it. Could have done a little more, though, since I find SS:BFBB more fun.
Paper Mario: The Thousand Year Door - Some of the best gameplay, one of the the best stories, and some of the most entertaining characters found in a Mario game.
Age of Empires 2: One of the first games that I've poured hours upon hours on. My favorite RTS.