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I have site that has been around since 1998. It has always been a PR5 with a DMOZ entry and some good links. It's a review site and has built up a fair amount of original content. About three months ago I moved my blog from Blogger over to this site and merged the two (isn't Wordpress wonderful!). This has given me the chance to observe the indexing of pages.
What I have found is that Google will only index three levels down and no further. The rule seems to be absolute. My site structure means that my monthly archive pages and category pages are level three and these are indexed but the posts linked to on those pages are not. So my individual posts were disappearing and/or going Supplemental after they left the front page.
The other significant thing I've seen is that the reviews from the old static site were going supplemental or disappearing. The link to these pages are on a level two page BUT this page now has more than 100 links on it (counting the navigation/sidebar). Two weeks ago I decided to take action and split that page up into individual years. Suddenly I am finding those old reviews back in Google.
In the old pre-2005 Google, all of these pages were indexed. I have to admit I resent having to spend days re-organising my site structure just for Google (Yahoo indexes my site fully).