Everyone would expect me to say Super Metroid but I go with Metroid Prime one by a hair. The atmosphere and pace of the game was great as well as the story which was optional. Super Metroid is by far the best 2D and I know the game inside and out but Prime was more fun to me.

They need to make a new Super Metroid on Gamecube with high res 2D graphics and new everything. Same floaty jump thing also. That would kick so much ass.