Today I was researching some modules for a large project that I am working on and I came across the Context module. This module allows you to setup different conditions and add/remove content from the theme. For example, if I wanted an entire block region removed from a members only region of my site, I would setup my condition to be 'intranet*'. Then, I would set my 'Reactions' to remove the proper template regions from the theme.
Pretty badass!. I'm going to continue learning about this, and will post more as I get deeper into the build of this new project.