If the duplicates are all in POP accounts then it might be to do with Exchange 2007 and not Snow Leopard. I found a few websites that discussed the duplicate mails for both Macs and PCs using Exchange 2007. For example:
http://hms.harvard.edu/hmsit/pg.asp?pn=email_preventduplicates
This happened to me when I installed SL at home. I thought it was a SL issue until I went to work (which still runs Tiger) and I found that the duplicates had arrived there too. When I looked at the duplicate mails in on my Tiger mail - I found that there were very minor differences in the duplicates - eg. in one email the sender was "Bob Brown" while in the second email the sender was "bob.brown@XXX.com" - it is almost as if somehow the mails left on Exchange were recognised with a different code. It seemed rather a coincidence that it all started when I installed SL. So I think that the connection between SL and the Exchange server sparked off that difference in code recognition?? Exchange servers are complex creatures which I don't claim to understand them.
And some people in this thread seem to have had duplicates with IMAP as well and I don't understand that one either.
But I can offer one work around to the multiple emails. If you create a smart mail box with the single criteria that all unread messages go in there. When the duplicates come in you can at least save time and delete the duplicates easily from that smart folder without having to manually identify the duplicate mails.