Rob Allen, who is on PHPWM and who I met at the recent PHPWM meeting in Worcester posted something on his blog detailing his prefered directory structure recently.
Here's mine, seemingly nicked straight from FHS:
/home/$USER/www/$PROJECT:
/codebase
/bin // anything with a shebang in
/etc // config files
/htdocs // document root
/lib
/class
/function
/sql // MySQL dumps with data
/tmp
/cache
/var
/log // just app logs, not server
Everything in /codebase is under version control.
All apps are served from respective home directories. Each developer has their own local Bind zone, their own httpd.conf (with a correctly configured sudo so they can edit it themselves) and each application has a single global settings file that can work out the user running the code so the paths are the same and it should Just Work in a multiple developer environment.