Recently, I've been checking out some of the blogs that link back to me because they use one of my plugins. And it seems like a lot of them are using buggy, incorrect templates. It looks like many WordPress theme developers don't read the theme development checklist.
Another fine document that some developers seem to ignore is the list of plugin API hooks. Please, read that section, and include these hooks in your template! Some plugins need that API hook to work at all. My surprisingly popular snowstorm plugin for example certainly does.
While you're at it, think about how you want to style, for example, the wp_footer() call. When I visit pages that give me a backlink through that call, sometimes the backlink is displayed in very odd places and with weird colors.
Finally, although it has already been said on the pages I linked to, get the theme unit tests and use them! It's quite embarassing for a designer to release buggy WordPress templates.