When writing a prototype web application I ran into a similar issue, for me paths were the crux of the matter, and urls like http://my.test.server/webapp/path/to/my/favorites to be much more sensible than http://my.test.server/cgi-bin/webapp.pl?path=/path/to/my/favorites

The modperl pages are a wonderful resource. Specifically you might like to look at Location & SetHandler which can do what you need. Getting your admins to hack on the httpd.conf for you is an excersise for the reader :).