I've be using Starkers for a while but I wonder if there are blank/naked themes with better code, files, and folder organization (based on Wordpress coding standards)?
I used whiteboard and Refuled but i think you can take any blank theme, and do some fine tuning to it in order to turn it to your own blank theme. For example, remove functions you dont need from the functions.php file, and make sure to reduce any unused CSS rules and to better reset the CSS.
I would also take a look at the HTML structure to see it contains DIVs for content and ULs for navigation as standard coding. Of course, you should also perform HTML and CSS validation (by W3C).