Hey Joe,
I noticed the same thing (large drop in indexed number/percentage of pages) a few days ago and thought that was related to a ranking drop I have experienced. All I did was resubmit all (tag, category, posts) sitemaps via GWT and the next day Google had almost 100% of my submitted URLs back in the index. However, that didn't fix my apparent Google penalty issue so I'm still searching for a solution:
http://www.seomoz.org/q/help-with-diagnosing-google-penalty
Oh, this was with a wordpress site utilizing Yoast's WP SEO plugin to create XML sitemaps.
