Wisdom from Logs
By now you've already seen Google's version of its indexing, in Google Webmaster Tools, but it's a very good idea to look at your web logs diretly, to see the path Google has taken, what files he's viewed, what unexpected paths he's chosen.
Also look at Google's links for your site, by typing link:[your_site_domain] into a Google search box. You will see every page Google has indexed, and which ones are missing from the list.