Here's some info that may be of interest.
Drive straight with encoders:
http://www.chiefdelphi.com/forums/sh...89#post1446789
Use motion planning for best results:
http://www.chiefdelphi.com/forums/sh...ad.php?t=98358
http://www.chiefdelphi.com/forums/sh...d.php?t=134965
Do some simple system identification[1]. For example, take the wheel diameter problem Todd mentioned. Drive the vehicle in a straight line (by tweaking the left-right motor commands) and note the ratio of the left and right encoder values. Use that ratio to fudge your setpoints, or use it to fudge your encoder readings before using them as your process variable.
[1] http://en.wikipedia.org/wiki/System_identification