Recently, I changed the IMAP daemon used in IEAA server from UW-IMAPd (which is using mbox format) to Dovecot. The transition is easy, but not trivial as I originally expect. Here are the steps if you want to do so:

• apt-get install dovecot-imapd, usually, your old imapd would be removed
• then, edit /etc/dovecot/dovecot.conf, simply change the line protocols=, to make it support for imap protocol on 143 port
• make sure default_mail_env = mbox:%h/mail:INBOX=/var/mail/%u, which should be suitable for most cases
• now the most tedious thing: for every user, go to his home directory
• create the directory ~/mail to store the users’ own mail box (non-INBOX boxes)
• create ~/mail/.subscriptions to list the mail boxes, which is exactly the same function (and format) as ~/.mailboxlist, so you can simply issue mv .mailboxlist mail/.subscriptions
• move the old mbox files to ~/mail

Done.

BTW: If you’re using any IMAP clients (e.g. Mozilla), better clean up all their cache or otherwise, there would be some strange behavior on the clients.