Actually POP messages may be still hiding if you know which mailbox they ended up going to.
Users -> yourname -> Library -> Mail and Mail Downloads folders stores the POP messages on your account from Mac OS X Mail in there only files that represent your mail folders. Other mail software may be stored in different folders.
A simple text editor such as Barebones Textwrangler can do a multifile search of the folder to see if you can find keywords from those messages and which folder the message resides in. If you actually did the message, the only way to recover it would be for the backup not to have overwritten in, in between. Time Machine's backup are recursive, but overwrite if there is insufficient room to keep all revisions.
If Textwrangler can't find what you need from either the Time Machine drive or the original, data recovery software as described below may be able to:
http://discussions.apple.com/docs/DOC-1689
Any messages you sent may be in the mail server logs of your internet provider. If you know the time you sent a message, they may be able to recover it from their outgoing mail server.