The Penguin update "ended". Like Panda, and others before, it was just an update (and not an on-going filter or a change in algorithm). There will most likely be another update, but it's impossible to predict when, only Google knows. So, the update happens, certain things get re-evaluated and this effects rankings. There's a knock-on effect; it's like dominoes as once you knock one over it hits the other ones that are in its path. So, your site might be clean but another site linking to you isn't for one reason or another, so there is less weight for you than before. So, people need to stop screaming, analyse everything (what you did, what anyone else did for you, etc) and fix what's possible: on-page, link sources, etc. The most important is your own on-page, but get some totally non-SEO people to review your site as well as do your own audit. Evaluating one's own work can mean we miss things other people won't and we can't forget the human factor; our visitors. Once your own on-page is sorted, then make sure the type of links you get are good (and this doesn't mean "high pr", it's a number you need to forget, but from sites that aren't spammy in their on-page or own backlinks). For those who think Google has a hidden agenda against them, this article is well worth reading (even if it's just up until the bit about 1996, but the rest is good too). One thing to keep in mind is that when the next update happens, if you've done a clean-up, you could go back up in rank and spammy sites above you will be pushed down. (Remember: if a site goes down, then another needs to go up.)
I have no idea when it will ends but now after google penguin update i start focuses on putting good unique quality content in my sites and trying to get quality backlinks for my sites.