I doubt Metroid Prime counts... But I'mma say it anyway.

Quake all the way baby!

The game that actually made the FPS scene explode back in the days. I am so sick and tired of all the FPS games of today, I miss the action packed Quake games. QW, Q3 and QL are certainly the top of the genre IMO.

Half-Life, unfortunately Valve won't jump off its pile of money which they call Steam and finish the damn series.

Goldeneye 007 N64
Goldeneye 007 Wii

1. Metroid Prime
2. Bioshock
3. Half life 2

Metroid Prime, Portal and Half-life. And those franchises are not precisely in healthy times...

My favourite FPS would be ( In no particular order ):

1. Halo
2. COD
3. Battlefield

I also enjoy an FPS game known as Be Gone, it's a very restricted free online shooter ( Less weapons/maps when compared to paid console/PC FPS ) which I honestly quite enjoy to play every ounce in a while.

Half-Life

Yeah but it's just a port. I was kind of hoping for a an HD remake but this is good as well :) Hopefully the controls are fixed and modernized. They need to be very careful when they do this or do a sequel. It's going to be weird seeing it on a non-Nintendo platform and while it's okay for them to continue the realistic environments and maybe enemies. The main characters should not have their looks "modernized" or changed up much. This would not impress a lot of fans as that is the core essence of who Juno, Vela, and Lupus are. I also wouldn't want a full on cartoony or anime look either. They need to find a balance between these characters and the environment, the original game did this very well.

Quake 3 Arena is my favorite FPS, so that one. Second is Wolfenstein. That poll makes me feel old.