I believe the Jak & Daxter trilogy is the true platformer game. The story line did a great job at pulling me in.
What is yours, Flood?
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Hm, that's tough, it's really mostly down to Nintendo games for me. My favorites are: Super Mario World Super Mario 64 Super Mario Galaxy Donkey Kong Jungle Beat Donkey Kong Country Returns (best DKC game, yeah I said it) I also really like LittleBigPlanet (floaty physics and all), Sonic the Hedgehog 2, Kirby Super Star, and the Rayman games.