I've been using clamscan (part of the Clam Anti Virus package; OS X version available via Fink) and Apple's Mail for quite a while now. However, I never really had an 'elegant' way of scanning my emails -- I'd scan my entire email folder as a crontab item:
/sw/bin/clamscan --recursive --move=/Users/*username*/.Trash/ \
--log=/var/Log/Clamscan.log /Users/*username*/Library/Mail/
This meant that, although the job would be done, the same files would be rescanned, making for an inefficient process. All that changed after I found Joseph Sacco's AppleScript. Although the script was designed to be used with ClamAVScan, it works well with clamav.
This modified code works with the Fink-installed version of clamscan.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050927050215641