I like *nix file system organization and always replicate such structure inside every project, so I use the following skeleton:

/home/httpd/<project>/bin        # cmd line scripts
                      cgi-bin
                      etc        # site configs
                      html
                      lib        # local libraries
                      tmp
                      usr        # read only data
                      var        # variable data files
[download]

This structure is well described in Filesystem Hierarchy Standard. There was a really interesting thread on mod_perl mailing list (OTish) Version Control?, where were discussed many related issues (iirc: testing, deploy, local modules, cvs). Look also here: Developer's Directories Tree.

Ciao, Valerio