Dunno so much about the automagical part of the question - you need to put some effort into coding a few things first :-)
Look at CPAN, particularly modules like Net::POP3 or Mail::IMAPClient to download messages from a server or Mail::Box to access mailboxes, Mail::Internet to grok the messages, MIME::Parser to handle attachments and the relevant DBI module to stuff everything into a database.
Cheers.
BazB.
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