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 use a similar layout, but with one major exception: all of these directories live under a top-level media/ directory. This is for a few reasons:
A custom template tag (I have used this with 2 Django projects, but you could do it in PHP, etc.) generates urls which a) semi-randomly choose one of the media servers, b) add the time-based pseudo directory to the path, and c) give the object an Expires time of now + 10 years.
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.
I definitely love the idea of having a skeleton template folder like this, but if you use a few different technologies, definitely pay close attention to the structure. My VB.net folder structure has a totally different setup compared to PHP. It sounds like common sense, but I have seen people approach both the same way.
I think what you have here is great.... What you've listed is of course all about the public front end of your app. My only addition to this, is to keep all your backend code and source out of the public web space if possible, as the less things you have in the public space, the more secure your app is.
So I'd suggest you take your entire tree, and put it in:
httpdocs/(all you had in your project template folder)
then put all your backend code (e.g. php libraries, sql files, etc) in adjacent subdirectories:
httpdocs/(all you had in your project template folder)
phplibs/
sql/
etc.
And, even for your front end stuff, make sure you don't copy in any example files that may come with your front end libraries, as the examples themselves may have security problems that would allow people to XSS or otherwise compromise your site.
I like OPs as a default start point. your standard template should err on simplicity, with the ability to add complexity only if it's needed.
one addition:
/robots.txt