This is an excellent start for the boilerplate converted into a WordPress theme. I would like to add the following for you to consider:

http://digwp.com/2010/03/wordpress-functions-php-template-custom-functions/ – My favorite inclusion to the functions.php file is removing the unwanted crap from the head as well as putting threaded comments in the functions.php (to keep the head clean).
http://digwp.com/2010/04/wordpress-custom-functions-php-template-part-2/ – Completely removing version number from installation. Very good security practice to follow.
There’s lots of other good stuff to reference on digwp.com as well, but these are the things I immediately include.
In your boilerplate admin, you should provide a checkbox option to include asynchronous Google Analytics code to the head, with a field input to easily add the account number. If checkbox is enabled, it can put the code at the bottom of the head.
For those not interested in using the Modernizr project, adding a link to the CDN version of the HTML5 Shiv would be a great option (with a note explaining to use one or the other.

These are the most important notes I can contribute. Thanks for your hard work on this!