Well, I have a PC and I prefer play FPS with a joypad (not on PC, on XBox) - mainly from a comfort point of view.
And obviously, if you have an online deathmatch between a team of joypad users and keyboard/mouse users the latter will clean up. This doesn't prove that it is an overall better control method - just that it is easier to aim - but who wants games to be easy?
I played Halo on the PC after playing it to death on the Xbox and it just felt too easy to pick off headshots and I had to ramp up the difficulty just to have a decent game. Also, I couldn't believe how much easier FPS games became once I finally invested in an optical mouse.
Basically, if a game is designed to played with a mouse then that is how it should be played and vice versa with games for joypads. That's one of the things I hate about online PC gaming. You just know that there a guys out there with specialist gaming equipment like variable DPI mouses/mice(?) and configurable keyboards.
I'm happy with my Xbox live FPS - so much easier. Just don't challenge me to a game with your mouse and keyboard because we all know what'll happen...