The only problem is moderating the pop3 account. I am looking into a similar solution that would use a daemon to monitor incoming email. However since we use qmail, it would not be necessarily portable to other systems.

This daemon would call a PHP script everytime a new message arrives and feed it the message. This would then put the message in the database properly. Using a CRON job can cause your messages to get out of sync and create confusing threads. The best way to do it automatically is through a daemon.

There would be no reason to send the userid with the message because you will have the email address in the "Sender" field of the email. If it isn't an address from a valid vBulletin user you simply send back a auto-response saying that the message wasn't allowed and send it to /dev/null. This is the same way YahooGroups (formerly eGroups) works.

Basically I see a clean header looking like:
#XXXXXXX This is the thread Subject

Where the XXXXXX represents the Threadid. There is really no reason for anything else to be included. With the Threadid you can put it where it belongs and with the email address in the "Sender" field you can match it with the user.