I've had a thought. Maybe it should be a new thread, but it does tie into the idea of perceived "false positives."
A lot of people badly hurt by Penguin have "no manual action" emails, post-Penguin. If Penguin is mainly about spammy backlinks, you would expect affected sites to have gotten "unnatural link" notifications. Possible explanations:
--Penguin is about a lot more than that, maybe more subtle forms of spam or even any hint of SEO of any kind
--Some affected sites are hurt because their backlinking sites got hurt
In my own case, I don't think the second option could be the whole explanation. I have a handful of strong sites giving me quality inbounds, and then a bunch of little blogs plonking me in their blogroll - that kind of thing. It's possible the little blogs - most of which are on Wordpress.com or Blogger - got devalued, but that wouldn't seem to explain my 80% drop.
So in a way, I'm returning to my original theory in this thread: Penguin is about a lot more than backlinks. In fact, I think Penguin may represent a whole new way of looking at spam/SEO, just as Panda represented a new way of evaluating quality. I.E., a few years ago, you were either spam or you weren't. Then Panda came and you were either spam, lower quality content or better quality content. What is Penguin trying to sort out? Could it be trying to detect and punish ANY form of SEO - that is, even though Google said "aggressive spam" which sounds like "the worst blackhat spam" in my mind, what they really meant was "any attempt to do well by our algo at all whatsoever"?
And even then... I wasn't doing ANY SEO, so I still just don't get Penguin, or don't buy what Google has told us about its intent.