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
I have been using the following setup for a while now with great results:
/source: Contains any comps, notes, documents, specifications, etc.
/templates: Start here! Create all static templates that will eventually need to be ported into the CMS or framework of /site.
/media: Images, downloadable files, etc. Organized as necessary
/style: I prefer modular CSS development so I normally end up with many stylesheet for each unique section of the website. This is cleaned up greatly with Blender - I highly recommend this tool!
/vendor: all 3rd party code (jQuery, shadowbox, etc.)
Blendfile.yaml (for Blender; see above)