The penalty hit many a folks quite hard at around the new year, see: Rank #2 to Rank #6. Is It A Google's Penalty?. The issue had been the hot topic on many blogs and forums, strangely enough, earlier when Matt was quizzed on the issue he had said that he wasn't quite aware of the issue. Recently, Barry had written a post about it.
Now there is official confirmation about the reversal of the position six penalty from none other than Matt Cutts. In a thread at Sphinn and on the topic Matt explains, Ă˘â‚¬ÂťWhen Barry asked me about "position 6" in late December, I said that I didn't know of anything that would cause that. But about a week or so after that, my attention was brought to something that could exhibit that behavior. We're in the process of changing the behavior; I think the change is live at some datacenters already and will be live at most data centers in the next few weeks.
In general if you think a site might have a penalty (perhaps from past behavior) and you think the site is clean presently, you can do a reconsideration request in our webmaster console to ask Google to take another look at the site.Ă˘â‚¬Âť
The issue was on several forums and it's good that Google gave it the attention it needed. For those affected, there's nothing to worry about and Google should automatically fix it.