So the particular algorithm that people are interested in on June 27th and July 27th, those particular algorithms have actually been in line for over a hear and a half. So its actually data-refreshes that you are seeing, that are changing the way that peoples sites rank. In general, if your site has been affected, go back and take a fresh look and see if there is anything that may be exceedingly over optimised, or maybe that I have been hanging about on SEO Forums for such a long time that I need to have a regular person comment, take a look at the site, and see "if it looks ok to me"
This is a direct quote taken from a transcription of one of the videos Matt Cutts has been doing recently. Sure seems to me he is saying that if your site was affected, itís due to optimization. We had several sites affected, but eventually all came back; our suspicion is that they dialed back these over optimization filters. However, we also firmly believe they will be back. Who really knows, but we have been taking a hard look at too much commonality in the title, H1, text and percent of incoming anchor text all matching up.