The mail for an individual cPanel account is stored in
/home/$username/mail/$domain/$mailbox/, while metadata for the account (mailbox passwords and quotas) is stored in
For migrating a full domain to another account or server, copying these two folders and fixing their ownerships is sufficient to enact the migration. In addition, there are a few bonus files to look at:
These are, respectively, autoresponders, SpamAssassin settings, SquirrelMail settings, horde settings, and forwarders. Each of these metadata files will add to the completeness of your mail migration, making a smoother experience for the clients when they start using the new server.