I agree with what Masem said, but I'd create one config file per virtual domain or virtual host. That way if you move one domain to another host, it is easy to move its config file rather than editing a big one. I agree that XML is the way to go, both for readability and for maintainability. Something like the following might be a start:

<config vhost="my.virtual.hostname">
  <script name="some_script.pl">
    <logfile name="/wherever/some_log" />
    etc
  </script>
  <script name="another_script.pl">
  etc
  </script>
</config>
[download]

Check CPAN for some modules that help you parse XML. I especially like XML::Simple for config files.
HTH, --traveler