I have posted my directory structure and comments in another thread, but it is applicable here too!
I have been using the following setup for a while now with great results:
/site: This is where my actual working website will live. I'll install my CMS or platform in this directory after the templates are created.
- .htaccess (basic tweaks I usually find myself enabling anyway)
- robots.txt (so I don't forget to disallow items like /admin later)
/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.
- /_behavior
- global.js (site-specific code; may be broken out into multiple files as needed)
/_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!
- print.css (this eventually gets blended, so use @media print)
- reset.css (Eric Meyer's)
- screen.css (for @media screen, handheld)
- additional modules as necessary
/_vendor: all 3rd party code (jQuery, shadowbox, etc.)
Blendfile.yaml (for Blender; see above)
- template.html (basic starting template; can be copied and renamed for each unique template)
/tests: Selenium unit tests