IMPORTANT: The accepted answer was accepted post-bounty, not necessarily because I felt it was the best answer.
I find myself doing things over an
My web development framework sits in a git repository. Common code, such as general purpose PHP classes gets developed in the master branch. All work for a particular website gets done on a branch, and then changes that will help in future work get merged back into master.
This approach works well for me because I have full revision control of all the websites, and if I happen to fix a bug or implement a new feature while working on a branch I can do the merge, and then everything benefits.
Here's what my template looks like:
/
|-.htaccess //mod_rewrite skeleton
|-admin/ //custom admin frontend to the CMS
|-classes/ //common PHP classes
|-dwoo/ //template system
|-config/ //configuration files (database, etc)
|-controllers/ //PHP scripts that handle particular URLs
|-javascript/
|-tinyMCE/
|-jquery/
|-modules //these are modules for our custom CMS
|-news/
|-mailing_list/
|-others
|-private/ //this contains files that won't be uploaded (.fla, .psd, etc)
|-.htaccess //just in case it gets uploaded, deny all
|-templates/ //template source files for dwoo