So you want to create a WordPress theme from scratch. But most blogs or sites have a similar layout – a main column for the content, and a sidebar on the right or left side for blog-related links like categories, pages, archives, etc. So why not start with a template that at least takes care of the raw layout for you?
Will at Tomorrow’s Laundry has created four blank WordPress themes with a two column layout that you can use as a foundation for your site. He has two fluid themes, and two fixed themes, each with a right or left sidebar.