Just to expand a little on neilwatson's answer, Anonymonk, you've got the problem backwards. More likely than not, you don't want to write a perl program to poll a mailbox for new messages. You'd be much better off hooking something into your mail delivery process (procmail is the most common way to do this under *nix) which can detect relevant messages and call your perl as needed.

One other thing: I started setting up something like what you describe once, a few years back. I quit just as it was getting to the point of usability because I realized that, with the ease of intercepting and forging email, it would be a major security risk. Consider whether your goal can be achieved without emailing commands around and, if not, be extremely cautious in your perl code. Use taint. Read all the standard precautions for securing CGI code and use them. Make sure you're using taint properly. Then go back over it and make sure you haven't missed anything.