Keyboard/Mouse: 9/10

Wiimote: 8/10

Gamepad: 6/10 

9/10 mouse(+keyboard)
7/10 wiimote (would be higher, but first we need some examples of games nailing the control)
5/10 gamepad (only this high because of goldeneye)

Wiimote: 9/10 (very realistic)

Keyboard/mouse): 8/10 ( much precision , but no so realistic)

Pad:4/10(Neither of the other 2 points) 

        I would give the Wiimote a 10/10.  Those of you who say it's not very accurate are simply not used to it (assuming you have used it before).  Once you get used to getting the Wiimote pointer on the screen, you will be able to do it and aim at a part of the screen faster and more accuratly than any other system.

        I would give the mouse a 9/10, although for how much I like using it for FPS I would give it a 5/10.  Its, in all honesty, too easy.  Now I do not want to contradict myself and say its easier than the Wiimote, it only has a shorter learning curve, but it is just too easy. Think about it, if you wanted to you could "aim" your gun at a spot on the screen, then be able to hold it there without even holding the mouse, it just sits there. Its rather boring and not a natural feeling at all.

        And finally, the analog stick or gamepad. Let me think, probably a 3/10.  I dont even know why it gets that high a score, I guess just out of respect for the thing I have used for aiming for my entire life.  Let me evaluate it.  It gives off no natural feeling what-so-ever. Its much more difficult to use than the mouse and wiimote and is much slower than the mouse and wiimote.  And, for the clincher, its the only one of the 3 that in everygame must be toggled on or have a button held to be able to actually use it to aim. The wiimote you just point and shoot at anytime.  The mouse you just...drag and click at any time. The analog stick in every game only is used for aiming while a button is being held, or has to be toggled on and off. Thats the worst part of it.  Then once you toggle it on or hold a button to use it, your versitility is shot.  You cant look around and move without stoping aiming.

For a first person shooter game I would always pick a gamepad over anything else, otherwise in a game like swat or something it would be completly unfair and no fun. Its probably just me but I'll take a gamepad over a mouse any day

Mouse: 10/10

Wiimote: 7/10 (because of games like red steel and farcry)

Gamepad: 6/10

In line right here...... 

Wiimote 8/10   After spending  about 30 hours playing shooters on the Wii were you can aim freely with the Wiimote I can say this is the best. With time and experience, I can easily get repeated head shots even in crazy environments. I can't say that about analog stick(not even with heavy auto aim) While I like the aiming with the Wiimote better it's looking around that's a problem. since the Wiimote is not a on a stable surface, one flick of the wrist and your all over the place. So I'm sure newer titles will fix this. really it's hard to compare the brand new Wiimote with all lackluster fps titles against the other two that have had more then a decade of great shooters to compare.

Mouse 8/10 Yes I rank it tied with the Wiimote, and while as pointed out above it's easier for movment it's simply more natural to point with your arm/hand at what you want to shoot, so it losses points two points in that respect.

Analog Stick/game pad 4/10 : I hate this setup, and only play along with heavy auto aim. But the fact that most Wii shooters don't use auto aim, and the analog sticks mostly do is simple admission to the lack of control with analog sticks. The prescision simply isn't there. and this setup has led me to not purchasing many games because of it. Like the fact that I'm debating on whether or not to buy Halo 3 simply because of this, yet if Halo 3 were on the wii I'd have preordered it already.

This one will be easy really.

Wiimote : 9/10

1 point lost, because though it's by far the easiest to get in seconds, the controls can be confusing when you're new to these kind of games. But everybody can grasp the concept right away, and begin playing even if they never touched a computer in their life.

Gamepad : 6/10

 Analog sticks are complicated to grasp. You have two of them to master, with your thumbs. Those are completely non-natural moves, that you take time to learn. It works so bad, the games have to put things like auto aiming for it to be acceptable. With increase in games display resolution, it can only be worse.

Mouse : 1/10

Completely unnatural, scare most people right away, and you need a long experience with moving a mouse (takes at least a week), clicking right or left, and you have to use the keyboard, which is very user unfriendly for games. That's the worst control of all. No wonder people gloat about mastering these, as it's so complicated. 

People that want to have fun, and not learn lots of complicated things before having fun, will go Wiimote right away : best control ever for FPS. Must be why arcade cabinets have light guns and the like, and not mouse or gamepads...

It's also more natural, not like FPS with the mouse, where the viewer can do amazing things, like strafing as fast as he runs forward, make U turn while running (which should mean they can make saltos and all, but never do) against a wall without bumping the gun against the wall, regain health after some seconds or after walking on items, and things like that. What's funny, is that hardcore FPS players talk about physics in these games, despite all these nonsense.

Keyboard & Mouse - 9/10: The keyboard and mouse is one of the most unnatural input methods for 3D space but since we use the mouse so much for screen movement and the keyboard so much for typing it ends up being one of the most accurate and easy to use. In other words it sucks but we are used to it ...

Wiimote - 8/10: Amazingly natural yet I haven't seen anything which demonstrates why it is better than a keyboard and mouse yet

Gamepad - 5/10: Unnatural and we (practically) never use the analogue stick on our right hand to map to 2D screen space so we lack the experience to do much with it.

 I couldn't have said it better myself.