My List:
1. Metroid Prime
2. Metroid Prime 3: Corruption
3. Metroid: Zero Mission
4. Metroid Prime 2: Echoes
5. Metroid Fusion
6. Metroid: Other M
7. Metroid Prime Hunters
I can't decide between Prime or Prime 3 for number 1, but for nostalgia's sake I'll put Prime on that spot! I loved the direction the Metroid franchise was going with Prime 3, though we lost the sense of exploration a little bit because of that. The ship interaction was just ingenious and I doubt anyone can deny it, plus the controls added a whole new dimension to ''being the bounty hunter'' under the mask. We finally got to play with Samus' toy! 
Metroid: Other M is not a bad game, but it's just too short for a console Metroid game in my opinion. I had a feeling the Prime games had a lot more in one package, plus they had memorable music at least.
Random game thought :
Why is Bionic Commando Rearmed 2 getting so much hate? We finally get a real game and they're not even satisfied... I'm starting to hate the gaming community so f****** much...
