I started up Mail.app (1.2.5 v552) today, and it asked me if I wanted to import mail from somewhere else. I knew this was a very bad sign, since it meant it couldn't find my existing mail data.
I say "No" and it starts up, I see the "On My Mac" folders which appear to have not lost any messages. However, my 5 POP accounts and the Inbox for each one is GONE. The only account left is my .Mac account which is still functioning and has all the old mail in it.
The only major thing I did on my TiBook 667 DVI yesterday was install the second version of 10.2.8. I doubt I will ever get back the mail that was in those inboxes, which is really the only major problem here. I can recreate the mail accounts, no big deal.
I think I'm going to try a different email client, or at least start with a fresh mail file to avoid any residual corruption.
If you have seen this problem yourself, or have any ideas on how to try and recover the lost account info and messages let me know.