If you use something like QMail, this is pretty easy since you can insert programs into the processing stream that could, in fact, be written in Perl. There is a wide variety of locations where you can hook in to the mail stream, and each provides different information.

As a cheap hack, you could just make something that smells like the 'rmail' program used by your mailer, assuming you're using something like the archaic 'Sendmail'. Your rmail program could, instead of delivering the message, put it into the database. Have a look in /etc/sendmail.cf for details on what program you're using. If this file makes no sense, use QMail.