When upgrading from my old G4 cube to my new dualie, I wanted to keep all the mail I had organized into folders (in the "On my mac" section of the mailboxes drawer). I found that I could simply drag the folders from Mail.app to the desktop. I zipped them up, uploaded them to my iDisk, set up the new computer, downloaded them, and dragged them to the On my Mac part of the Mail.app mailboxes drawer. So now I have all my old mail on my new computer.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20030904080956163