Wolfenstein will support joysticks. You must go into your wolfconfig.cfg file and change the line [seta in_joystick "0"] to [seta in_joystick "1"] , ignore the brackets. If the line is not there just add. This worked for me and enabled me to use my usual joystick/trackball combo. I just wish joystick support was more universal in games, but at least any QIII based game should support it.
Jim