There are a few things to consider about our overall crawl and indexing pipeline. As part of some recent updates (http://www.mattcutts.com/blog/bigdaddy/) we're taking a much closer look at affiliate links, linkfarms, duplicate content, and other factors as described in our webmaster quality guidelines.
As with the Florida update, when Google went after sites that were perceived as going against Google Quality Guidelines, some good & clean sites were hit in the cross fire. With this, the same has happened, and it will always happen.
So if you are suffering, you can try posting in the Google Group or emailing Google, as specified in the thread.
Forum discussion continued at WebmasterWorld.