Generating an eml file is somewhat more difficult than generating a msg file. There are several ways however to generate an eml file:
Through procmail: Just save the file to disk with procmail before it delivers to the dagent.
Through the MTA: E.g. postfix has an option "always_bcc", which you can misuse to always bcc an email to a user with an mbox mailbox.
Through zarafa-dagent: In ZCP version 7 the dagent has an option which will enable you to save incoming emails to an eml file in a certain directory. Check the config options "log_raw_message" and "log_raw_message_path" in the zarafa-dagent.cfg manpage.