Not specifically perl related but some of this may point you in the right direction.
1) Run nmap against the box, find out what ports have something listening
2) run lsof -i to find out what programs are bound to those ports
3) take a look at the xinetd.conf stuff, find out what may be started when a port is hit
4) take a look at /etc/rc.# and find out what is getting started. Figure out what the # is by looking at inittab
5) take a good backup of the box, make sure it is a good backup of the box. Check the backup again. (including sane database backups) Then blow the box away, re-install it, and wait for people to complain about missing things. :)
6) Take a look at the site_perl directories to find what perl modules have been loaded on to the system.

With all of that, you may still miss stuff. But you should be able to catch the important things.