The more semantic you make your HTML, the less that this tends to matter. Right now I'm actually <section>ing and <article>ing my way around my site, so when I want to change the design, I head straight for the one place it's actually described: the CSS.
Not to mention the template mechanism. With my (home made) site generation tool, I changed the whole design of my site by changing exactly 2 files : the template, and the css.
