I too am trying to get my controller working how I want it. I use a Logitech Dual Action, which I use for FPS, namely, Halo PC through Windows XP. Halo PC is gamepad friendly, most FPS games are not. On Windows, I have used Logitechs own Logitech Profiler software to use the controller with Urban Terror (a Linux compatible FPS based on I think UT), and I have used a program called XPadder as well. These programs both are capable of tricking the software into thinking the gamepad is really a keyboard, and the right joystick axis as a mouse, thus enabling gamepad support for games that do not come with it.
I have just downloaded Urban Terror for Linux, and am hoping to be playing it with my gamepad soon. I used a Linux program called jscalibrator to recognize and calibrate the joystick, but that does not help me much into using the gamepad with a game such as Urban Terror. So, I also downloaded a program called joy2key, which is supposed to do exactly what I want, but I have not had success using the program.
Well, not trying to jack your thread, but I would definitely recommend the Logitech Dual Action controller, though I have little experience using it with Linux. It is practically identical to a PS2 controller. I have had mine for years and it still works good. Im not sure if the OP had binding the gamepad to keyboard/mouse, but I think it is generally useful to do, and personally, I would appreciate any advice on how to do this in Linux.
System: Gigabyte AM3+ mATX mainboard in Silverstone FT03 case, AMD Phenom II 980BE 4core @4GHz on a 2600MHz bus, 8GB dual channel 1333MHz CL6 RAM, nVidia GTX56Ti-2GB, WD Black 500GB w/ #! Debian and Xubuntu