In a thread at SEORefugee, while discussing a site that is having the dropped pages problem, Michael (mvandemar) brought up a point that I think should be considered. He said in post #15:
Do a link: command in MSN, and then go through those results, and try to get an idea of how many of those are cached in Google. With the large number of sites dropping from G's index, you may well have lost a large portion of what was powering you before. It happens.
Even if you have a squeaky clean site, with perfect quality links, you may have lost some of those quality links if pages on which those links were placed were dropped. Remember in the days of frequent PR updates, when for some reason pages on sites like DMOZ would drop from say a PR7 to a PR6, and all of a sudden tons of sites would lose PR as well? We all understood that one site's loss could cause lots of other sites to lose as well. The same might be happening with dropped pages.
If quality links are now a prerequisite for getting a page in the index, and you lose a quality link because the page the link was on is dropped, then you may also lose your page because you lost the link. Make sense? And if lots of pages are dropping out, you may be losing lots of quality links. It may be one big domino effect.
Just a thought. Something to consider if you have looked at every other possibility.