Being a catastrophically stupid gremlin with regards to computers, I somehow managed to get tons of 'ghost' duplicate messages when importing old mailboxes into Tiger's Mail.
The content of these messages bangs on about a failure to download the original 'from server,' even though the original is universally sitting, threaded, just above or below the 'ghost.' I'm sure someone will be able to tell me what I've done (please), but a quick fix is the following...
Construct a Smart Mailbox which excludes mail from all your real mailboxes -- Inbox, Sent, Import and so on. Insofar as the 'ghost' duplicates are identified by Mail as residing in no specific mailbox, they will be grouped in this new smart mailbox, ready for deletion.
Mac OS X Hints
http://hints.macworld.com/article.php?story=200505040649362