Some shameless self-promotion: Rolf and me are going to teach a special one-day class on BinDiff 2 at BlackHat Las Vegas this year:

http://www.blackhat.com/html/bh-usa-06/train-bh-us-06-hf-sabre.html

We'll cover applications of BinDiff to malware analysis, detecting Code Theft and GPL violations, and of course the usual patch analysis.