Actually, I'm not sure if I understand what you're after ...
If you want to wrap the output of a Perl (or whatever) script into Geeklog (i.e. have the header, footer, and blocks of Geeklog but the output of the script in the middle of the screen) then that can be easily accomplished:
require_once('lib-common.php');
$display = COM_siteHeader('menu');
$display .= COM_startBlock("My CGI Output"

;
$display .= `/path/to/your/perl/script.pl`;
$display .= COM_endBlock();
$display .= COM_siteFooter();
echo $display;
Put that in a .php file (and don't forget to add the opening and closing PHP tags).
Is that what you're after?
bye, Dirk