With <Perl> ... </Perl>sections, you can configure your server entirely in Perl. It's probably not worth it if you have simple configuration files, but if you run many virtual hosts or have complicated setups for any other reason, <Perl>sections become very handy. With <Perl>sections you can easily create the configuration on the fly, thus reducing duplication and easing maintenance.
You may also find that mod_macro is useful to simplify the configuration if you have to insert many repetitive configuration snippets.
To enable <Perl>sections, build mod_perl with:
panic% perl Makefile.PL PERL_SECTIONS=1 [ ... ]
or with EVERYTHING=1.