1. QuickPar Little known fact - QuickPar, the incredible par2 utility, can easily be set as the default md5 checker on your system. If you aren't creating new md5s - and who is, now that flac has arrived? - it's a great choice. http://www.quickpar.co.uk/
2. md5summer Handy for creating new md5 sets; though if you have mkwACT installed, it can easily be set to do the job too. But then, you should be using flac for new seeds, friends. http://www.md5summer.com/
etree.org's page mentioning MD5check See the fourth bullet, "Verifying the ffp.txt is really easy ..." http://wiki.etree.org/index.php?page=FlacFingerprint