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 a similar structure and naming convention but for CSS, I use BluePrint which I find is more extensible. Also prefer jQuery having recently switched from prototype. In addition I have a common.js file that is an extension with custom functions for jQuery.
A /db/ folder with .sql files containing schema definitions. A /lib/ folder for common middle-tier libraries.
I will also have a /src/ folder which will sometimes have raw files such as Photoshop templates, readme's, todo lists etc.