way back in the day, I used a joystick to play DOOM.
That was when you didn't have to worry about enemies jumping of ledges 100s of feet above you, only to chop your head off.
When I started to play JK and then into HL, I moved from just using my keyboard into a combo with my mouse. I find that a mouse+keyboard combo makes for the most accurate way to play any FPS game nowadays.
[Edit: I will mention that I know plenty of people who use a joystick in conjunction with a keyboard... not my best idea to play, but hey try it if you must]