i play quake3 with linux (debian etch 2.6.12.1, ms ie3)
i've tried almost everything but the mouse acceleration still remain... with the usb @125hz it is very small and it's playable... with the usb @500hz is pretty high...
i have "xset m 0 0" when linux start, "cl_mouseaccel 0" in the q3config.cfg
with ut2004 i have no problems at all

any ideas?