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
At work we use Code Igniter as a PHP framework for our web applications and have created a new project template which does exactly that: Simple directory structure, Blueprint CSS, jQuery and the Code Igniter application folder, filled with a couple of commonly used libraries (Authentication, some speciales models for often used databases...).
The main motto here is: It's always easier to delete components than to add them. So fill your template up.
(And when I'm starting a new project in my spare time I sorely miss that template...)