I have been meaning to post this for a while, but kept forgetting.
UrbanGiraffe published the last of his articles on “Dissection of a WordPress theme”. They are very good reads, and really can help anyone get a grasp on creating your own theme. There are three parts in the series. He has however created a “Theme Guide” section on his blog to organize everything he has done. And he has also made it available as a PDF download!