PatchDiff 2 by Tenable Security

Finally a free alternative to the insanely expensive BinDiff by Zynamics (also known as Sabre Security in the past). It's been developed by Tenable Security (the people behind Nessus nowadays), and requires IDA Pro 5.2 on Windows. Get PatchDiff 2 and give it a try, it's looking good so far. That said, it's graphing capabilities aren't as nice as BinDiff's, and it may lack of some features, albeit possibly compensated by the 1330 USD of a license to 0 USD of Tenable Security's free alternative.