Packing site to standalone executable file
There is an utility tools/packsite-par.pl included for creating executables from web server and the site itself. That utility uses PAR toolkit as backend. You have to install PAR and all its dependancies to be able to use that utility; there are caveats in installing PAR and choosing version of Perl to use with it listed below.
Stunnix Advanced Web Server package includes a sample site and scripts to make multiplatform CDROM with site on it (with autorun support for platforms where it's possible to have it) and also a sample for packing same site and Stunnix Advanced Web Server into standalone executable - see more details in Stunnix Advanced Web Server package overview.
Notes on installing PAR and choosing version of Perl to use
Notes on packing to .exe for unix:
Notes on packing to .exe for Windows:
Note on protecting your code from analysis
Even if your site is packed into executable, your entire site and Stunnix Advanced Web Server are extracted to the temporary directory once executable is run, and are available in the form they were packed in. So packing sites into executables shouldn't be meant as a way to protect code from analysis and illegal reuse. If intellectual property of your Perl code that implements logic of the site needs to be protected, the most recommended way is to use a special tool for making Perl source unreadable and much more difficult to analyze - Stunnix Perl-Obfus. In fact, Stunnix Advanced Web Server and Project Manager code are already protected with Stunnix Perl-Obfus.