I have used all three.

It is hard to quantify but I will do it anyways.

Mouse 10

It is easier to look around and the aiming is precise and quick also programmers can actually slow teh mouse look and aim to change the feel.

Wii mote 7

 For the time being aiming is a dream but turning can be hellish oops too far on the reticle now got to back. It is far more accurate than what I see people complain about but it is also sensitive to how far you sit from the sensor bar. It does eliminate the need for hitboxes. Personanly I hope tht if they ever do release the light gun attachment you will be able to use the nunchuck. Nintendo needs to place a calibration tool for the pointer so it can beter adjust for distance.

Dual Analog 3

It is slow it is sluggish. It takes too long to  line up your shot and the games compensate heavily for that. I find my self depressing the zoom button way to much. Resistance felt like a chore to me to aim and while Halo and Goldeneye were both playable they never quite matched Half Life or counterstrike on the PC for feel. the Dual analogs do allow for better movement than the Wii mote but it scores much lower because of aiming. FPSs can still be good but the game design has to be set for it.

I love that w/ the Wii there's no need for atrificially un-steady aim to seem realistic: since your aim is as steady or not as you are naturally. E.g. RE4-type wandering aim isn't needed to make your aim seem human / not robitic.

Mouse: 9/10

I haven't used anything that can beat the combo of a Keyboard & Mouse

Wiimote: 7/10

It still needs some work but I could see the Wiimote replaceing the Keyboard and Mouse. Right now its still early in its life and has room for improvement. (Ask this question again in a year or two) 

Gamepad: 5/10 (2/10 for the PlayStation)

Xbox, Xbox360, GameCube and DreamCast all had a layout that worked pretty well but no where near as good as the  Wiimote and Keyboard & Mouse.

PS2 controller gets a 2/10 because I absoluty hate using that layout for FPS, It's usable but barely.

PC FPS is probably my second favourite genre and type of game out of everything and honestly, I don't think that an FPS is about feeling like you are the person you are controlling through the use of a keyboard and mouse.

If we were going for the most 'realistic' method then I think the Wii would probably win, but in terms of ease of play and most fun to use and be most competitive with, then the mouse wins hands down.

I think it is fair to say that a dual joystick joypad really has nothing on Wiimote and Mouse combinations.

Me personally? I haven't experienced good FPS controls using the Wii yet and I honestly don't know if I ever will... You can't lift and move the wiimote like you can with a mouse and it feels less direct and more messy on the Wii to me.

In terms of competition and fair competition the Wii Remote leaves too much open, and I don't think it is possible to be as competative with the Remote over a keyboard and mouse.

Duck Hunt gun was really amazing. Exactly how did it work? No matter how long or hard I think about it, I cannot figure out how it worked.  You dont need any special TV, and you dont have a reference point (like Wii's sensor bar), so... HOW THE HELL DID IT WORK? Its amazing if you ask me. Someone please explain to me how this could possibly work. (not to mention the fact that it worked perfectly and flawlessly... amazing)

There is a white square around the duck when the trigger is pulled. If the gun detects the White square/flash. That means it was a hit. If it dont. It was miss.

EDIT: At least that's how I rembered it happend. Not gonna say this is correct. 

"When the trigger was pulled, the game blanked out the screen with a black background for one frame, then, for one additional frame, drew a solid white rectangle around the sprite the user was supposed to be shooting at. The photodiode at the back of the Zapper would detect these changes in intensity and send a signal to the NES to indicate whether it was over a lit pixel or not. A drop followed by a spike in intensity signaled a hit. Multiple sprites were supported by flashing a solid white rectangle around each potential sprite, one per frame."

Wikipedia 

Ditto, but I'll add some personal response too. I was always staying away from FPS before because I didn't think it looked fun and natural. I think it looks more fun, accurate and natural on the Wiimote. I might consider trying it one day!

Funny to see ppl comparing wiimote pad and mouse while the games are not the same. Oh sure, some games (like COD's) are released on several formats but in this case, they are always dumbed down to suit pad(or even wiimote).

 Just consider this :

In pure mouse/keyboard FPS, enemies are coming from everywhere (around, above and sometimes from beneath you). They move very quickly and the damage localisation is quite precise. Simply because the mouse allow very fast and precise aiming.

In pure Pad or Wiimote games, ennemies are usully coming slowly (sometimes remaining still) from the front (cause doing à 180° just take time), are dispatched on 2 or 3 even levels of high and most of the time, there is some kind of aiming assistance (larger cross, bullets following the target, etc.).

To compare these interfaces, you would have to play with them on a same, demanding, FPS, like Serious Sam on Hard difficulty setting. And my guess is that you would do well with the mouse, do OK with a pad, and just cry with the wiimote, because it's not just about aiming, but also moving and jumping around while following a fast target.

I normally play PC shooters, I never bought a Xbox/360 due to it using a Gamepad. So I'm a bit biased :)

Mouse/Keyboard - 10/10 it's almost perfect. The mouse points exactly where I want it to go, there is no real delay, it's smooth and sure. You also can get a whole range of Mice and keyboards so the tech is always improving which is what the PC is famed for. The only draw back is a lack of rumble or any other feed back.

Wiimote

Ah. I can't really "score" it as monkey wars is the only FPS I've played as I don't want to be put off FPS' on the Wii till MP3 comes out. But from what I've felt from using it as a pointer I can say it's lag is greater then a Mouse, and to me it really feels bad at first....but like online lag you get used to it and adapt. I  hope the next version of the Wii has one with almost zero lag.

Rubble,sound effects and actually pointing at the screen really adds a level of realism that I have high hopes for, but have to agree that the lack of re-centering might make mouse style play impossible to perfect. I believe thats why RE:UC is on rails.

Nunchuck - It's not perfect, maybe I'm crazy but I prefer keyboard, a life time of habbit is hard to break :)

running and Jumping just doesn't seem as .....fluid, but that just might of been Monkey Wars.

GamePad - N/A the idea of using a gamepad for a FPS is.....wrong. Tried it once. Never again.