CMS and the Supplemental Results index hell

Over the past month I have seen and heard about a lot of pages being put into Google's supplemental index. Most if not all of them have unique titles and description, unique content and no canonical issues. They even have prominent outside pages linking directly to these subpages. While reading some psotings on Digital Point forums I realized that all these cases had something in common, they were using some form of Content Management System whether it was Joomla or Wordpress.

The whole site carries the same header and footer and in some cases even the left and right sidebars are the same, I think this is pushing these pages into Google's supplemental index.

I'm still working on this one; Exactly how much content can you have on every page without it being classified as supplemental? Identical header and footer and a navbar.