The only game I use my gamepad on right now is Street Fighter IV. Keyboard and mouse is better for FPS or starcraft II, and I have a wheel and pedals for racing games, and a flight stick for flight sims. If I didn't have the wheel and pedals or the flight stick I would use the gamepad more though.
Games like Assassins Creed, Mass Effect, and Dead space work great with a controller (I use the XBOX 360 controller for my PC). However, you would have a huge disadvantage in MP FPS games such as Black Ops. As for FPS shooters in general, you could pull it off but you'll have to tone down the difficulty a bit.
I tried using my controller once playing Crysis...the results were similar to watching Richard Simmons working out in spandex, which is to say atrocious!
The advantage of a mouse over a gamepad is the to-the-point accuracy. With a mouse the accuracy in FPS games is far far better than with a gamepad. I have played COD on both ps2 and also PC and the difference is huge. The mouse allows you pin-point accuracy, whereas a gamepad does not.
In fps games on the PS3 there is aim assist. So it helps you aim and shoot people. No such thing on PC games. So you'll find it much more difficult to play for the PC. You may be able to do some FPS campaigns, but playing on multiplayer would be extremely hard. You can't turn as quickly, etc...
Just my thoughts. Controllers are good for racing games though!
Personally, I love using my xbox360 wireless gamepad with my HTPC. I've tried using the mouse and keyboard on the couch and it's so horrible. I would recommend getting one for any 3rd person game. I tend to play alot on my living room TV so I went gamepad. It's great for those and even some that are FPS. I play Mafia 2, Just Cause 2, ME2, AC2 and even FarCry2, Fallout 3 with the pad. I'm just so used to playing alot on the 360 that I had to get one to keep from losing practice. Then I found that I preferred it. I still keep a wireless mouse by the TV just to launch the game.
are you sure that you dont get aim assist on pc gamepads? im going to stick to the mouse and keyboard for a while and buy a good steering wheel for racing. i think that the steering wheel for pc is good in racing games. isnt it?
I avoid a gamepad in FPS games, but sometimes it's necessary.
I like to use my directional arrow keys for movement instead of AWSD and remap other functions around those keys + the additional buttons on my mouse. Some console ports restrict which keys can be remapped or don't allow it at all. In this case, I use a gamepad.
are you sure that you dont get aim assist on pc gamepads?
Sure there is, its called aimbot. All the "good" players have it on Bad Company 2!
But in all seriousness, most console FPS have aim assist. Like everyone else said, just try to play mulitplayer with a gamepad on PC and see what happens. But I think gamepads are great for other games on PC. Playing sidescrollers on KB is not fun.