Which is the best and why?

GE it isnt even a contest. It was original FPS (at the time) for Wii. pretty decent campaign. When the MP works(it had and has a few hiccups) its fun as hell. Golden Gun mode. It still has a very active community. A lot of control options, default motion controls suck but thank god they are heavily customizable ensuring that just about anyone could find a configuration they enjoy. The COD games are just worst versions of games that are already on 3 different platforms(yes one could say the same for GE but the HD versions werent release till a year later). Conduit has to be the most overhyped game on the system, maybe on any system this gen. I had MOHH2(PSP version) and its good, but isnt as polished as GE.

Other - Metroid Prime 3

Goldeneye by an epic long shot. Its campaign is endlessly creative, there are fun cheats for the local multiplayer, and it takes real skill to beat--especially on 007 Classic where you don't have the regenerating health anymore.

Goldeneye. It had high production values, great gameplay, and a multitude of game modes. I had serious doubts about the game and was pleasantly surprised that turned out so well. I wish more FPS games had single player campaigns that were as well crafted as Goldeneye's.

Other - Quake 1 via homebrew port.

I got to go with Goldeneye, the golden gun matches are too good.

Goldeneye for sure, metroid prime 3 is adventure first then FPS.

While the CoDs are excellent (for Wii FPS) they are still downports whereas Goldeneye was designed for the Wii exclusively (then upported to HD). Goldeneye is the most polished and highest production value of any Wii FPS.

Conduit 1/2 were fun, visually impressive (for Wii) but generic as hell. MoH:H2 was the best when it released but can't compare to CoD's/Goldeneye or even Conduit (multiplayer)

Metroid is FPA so I'm not considering it here. The only other worth mentioning is Red Steel - one has serious control issues and two lacked any multiplayer so neither compares.

Other.

I wasn't a fan of what Eurocom and Activision did to 007, and wartime shooters was never my thing.
 

 The way I see it, best Wii FPS is probably Red Steel 2. I wish the characters in the game was used a little more, and you might argue that it's more of an action game than a shooter, but it's dang nice to look at and really well paced. It's something different, and it's quite good at what it does.