Can I request a small change to the sidebar list of files when editing a theme...
All the files are listed a "Templates" header with the stylesheet separated below this under a "Styles" header. My suggestion word be for a new header added for theme functions, called "Functions" and the functions.php file listed under this.
I have made a quick mock up here: http://www.imageupload.org/?di=2129665814614
Optionally, both the style sheet and functions headers moved to the top of the page.