Here's what I'm currently using, although it's admittedly not CPAN-compatible, since I use git to deploy my webapps, so CPAN isn't a concern for them. Assuming I'm building My Web App:

• ~/src/my_web_app/
• TODO
• MyWebApp/
• (general project-specific modules defining the underlying object/data model)
• CGI/
• (plugin modules for connecting the object/data model to the web interface)
• cgi/
• index.fcgi
• tpl/
• (page-generation templates)
• (other misc files which need to be accessible by web)
• local/
• (misc host-specific support files which, for whatever reason, aren't put into the main git repo)
• t/
• (test scripts)
• util/
• (any command-line tools specific to the project, including cron scripts)

With this structure, installing on a new host is a simple matter of cloning the project out of git and symlinking the cgi/ directory into the host's web root. Depending on how the host's operating system handles paths doing a ../ from a symlinked directory, it may also be necessary to symlink MyWebApp/ into one of the dirs in @INC, but that's usually not required, thanks to FindBin. (Obviously, I only work with *nix-derived OSes. I don't know whether Windows has a suitable equivalent to symlinks or, if it does, what that might be.)

If I were to want to build a CPAN distribution out of one of these projects, I would expect it to mostly just be a matter of creating a distribution dir (call it dist/ and symlinking the relevant bits into it - MyWebApp/ into dist/lib/, t/ into dist/ to replace the default dist/t/, and cgi/ and util/ to... well... I don't know where because I've never packaged executables for CPAN, only modules.