Using JiTouch with synergy
The reason for this is that the Synergy server doesn't have an OS X frontend. I have the same issue with my Logitech mouse configuration -- I want to have a different scroll speed for Synergy because when I have acceleration enabled, the remote computer doesn't scroll properly. So I'd like to disable acceleration only when using synergy.

The solution would be to package synergys as an OS X app which, when you move your mouse to the remote computer, brings itself to the front (so that the menu bar contains only the Apple menu and a "Synergy" menu). I have planned for a long time to create such a wrapper which would accomplish this but just haven't had the time. 

I didn't realize others would be interested in the same idea... If I ever complete that project I'll be sure to let you know! Or, maybe we should file a feature request with the synergy project? :-)