Keyboard only. Keypad for all movement except look up, down and center view, which is Q-W-E. I shoot with the "A" key. I play(ed) all FPSes with the same setup -- Alien Breed 3d and Breathless (Amiga), Marathon 2 (Mac), Quake, Quake 2, Half Life, Half Life 2, Unreal, Return To Castle Wolfenstein and Doom 3. I almost always play Doom with Risen 3D, sometimes GZDoom, and more and more rarely, JDoom.
Most FPSes are kind of easy on Normal difficulty settings, equivalent to HMP in Doom, so it's not really a problem to ditch the mouse. On occasion, I do need to use the mouse to aim up/down in the 3D games, or to make a special angled shot in Doom. When that happens, I stand my ground and use only the mouse. I usually take a few hits that way, and sometimes I get stopped.
I realize that using the mouse would make it easier to survive areas where you get mobbed from all sides. But in a way, I like to keep things as they are, to keep the difficulty level higher. It's more fun for me that way. Also, I'm not into levels where you have to keep shooting at squillions of monsters, and shifting the screen too fast with mouse movements gives me motion sickness.
Nonetheless, I always play every level on UV unless I discover I cannot beat it that way, and then I switch to HMP. I guess it comes down to this -- I can beat all the Michael Krause levels on UV, but I know better than to even try something like Grime. :D