We use KERIO mail server, as a secondary e-mail server. KERIO stores the e-mails in directorys*.eml.
User1 mail box stored something like this:
2009\msg\*.eml 2010 Calendar Drafts ... INBOX\msg\*.eml etc
We are looking for a free / open source archiving software to export/archive the hole directory structure with eml files too.
For example I give a date to the software and this will export (and delete the original files) the directories till this date to an other directory.