An important choice to make is which mailbox format to use.
The traditional Mbox format consists of 1 big file per user. This is traditionally stored in the /var/spool/mail directory. This format is best suited to POP3 client access.
The Maildir format is much better suited to IMAP based mail clients as it readily supports folders. It consists of a directory tree, normally .maildir in the user's home directory. Each message is stored in it's own file which also makes the task of performing backups (and restores) much simpler.