Another vote here for the HTML5 doctype. Though I’m not so sure about the new elements.
Other things to consider:
* Support for a top-nav based upon Pages?
* Support for the OpenID plugin (eg so the comment form gets styled nicely if the plugin is added)
* Fluid-width rather than fixed-width.
* Abandon the comments-popup.php file.
* Do something more useful in the 404.php file (eg listing recent posts and/or offering a search box).
* Abandon the custom header image UNLESS this code is integrated into WordPress core – the functions.php should basically be blank, except for defining a sidebar and maybe declaring a value for $GLOBALS[‘content_width’]. The point of the theme should be to use existing functionality, rather than to add new functions (which should generally be done via plugins).
Frankie