Well I can tell you what I do.

I have worked out my own template system that uses a main wrapper containing, once included, header, navigation, right-panel and footer divs.

The content div is part of the main template. The other areas are included using the php include function. That way if any of these change, the change is immediately seen site wide.

CSS is used to take care of position and the look-n-feel.

The master template and the include files all use validated structured markup.