Nice! Are there any issues with running the xsp sdlquake in kde or are you running in non-xsp mode?

As for quetoo, I think the normal quake 2 needs autoexec.cfg line :
set in_joystick "1"

Assuming quetoo didnt rip out joystick support to make lean (like they did with the menus), you might try that... although if that does work theres alot of potential for complicated axis mapping which might yield better performance/accuracy.

For vnc or rdesktop I could see mapping buttons to browser fullscreen key, right click. I dont suppose you could map axis to mouse axis could you? Or would bluetooth mouse would work with KDE?