One of my sites was hit on September 4th, I came here and poked around a little and noticed others had also been hit around the same time with something.
So I figured I would come back and post this just in-case someone else was hit around the same time, and maybe this could help.
My sites are always pretty clean, so the penalty threw me off guard a little. Here are the before and after stats.
The only thing I did to recover was I started in the HTML Improvements area of Webmaster Tools and started cleaning up the errors. The area I think that caused the initial penalty, as well as the recovery, was the 404 errors. Once the 404 errors reached 0, two days later the site recovered.
This is just my opinion though, as everyone knows, with Google, it could be a million things.