Something I did know: Mail, under Panther or Jaguar, had a habit of not deleteing all my email off the server. As near as I could narrow it down, it seemed to be a matter of Mail not deleteing anything off the server that had been moved out of the inbox before it was done checking mail. (And I have many scripts that sort and move mail upon reciept.)
So occasionally I’d need to go into the preferences and clear all the mail off the server, assuming it was all old and duplicated.
Something I did NOT know: Mail in Tiger (OS X 10.4) allows you to do a GetInfo on the mail folders, and one of the options in the resulting window shows you the headers of all the mail sitting on the server for each mailbox, and even allows you to individually or mass delete the messages.
Though all the messages seemed to be from just one day a couple weeks ago.