I wrote a quick patch for the mbox-dedup.pl script I found online awhile ago. Basically, the author wrote a script that takes an mbox and creates a new mbox with all duplicate messages removed. I have to deal with duplicate e-mails constantly due to some weird incompatibility between Evolution and my Argosoft Mail Server (Windows), which I’ll have to figure out some day soon.
This script is just a temporary solution. I modified it so it now creates three files: $f.bak, a backup of your old mbox; $f, your new, dupe-free mailbox; and $f.dup, which is a mailbox which ONLY contains messages detected as duplicate. You can probably get rid of f.bak and keep f.dup around in case there were any mistakes in duplicate detection (which is what I’m doing). How annoying through. Anyway, if this bothers you, download the script, but use at your own risk.