That same command can be used to increase acceleration too.
Originally Posted by Anathaen
Play around with the values until you get something that feels comfortable.
xset mouse [[accel_mult[/accel_div] [threshould]]
I'm pretty sure that most acceleration configuration tools just modify these values anyway.
Okay, I think I misread your post.
You're having problems with the in-game mouse acceleration, not the desktops.
I've sorta experienced this in TF2, and turning off desktop accel and boosting mouse sensitiviy improved things, but I think the mouse accel code in Valve's games isn't that good yet.