Joystick 2 mouse lets you use your game controller to move your mouse around the screen, and a whole lot more. You can do just about any Windows function with this program, including typing (though this would be a nightmare), all from your game controller.
The reason I looked into this was so that I could control Windows Media Centre from my couch. I had all sorts of problems finding a suitable tool. Eventually I came across this gem. After installing it, I found out that it could do much more than I initially wanted. There is no reason why it could not be configured to control first person shooter games.
It is highly configurable, allowing you to change almost every aspect of it. You can use it to control any application. The only drawback I found was that there was no option to disable/enable this utility from the controller. Disabling it is possible by exiting the program, but without the program open, you can no longer use your controller to re-launch the program.
Logitech users would probably be best using the profiler software which can be downloaded from their website. This will allow similar functionality.