austtr - 11:48 pm on Oct 27, 2013 (gmt 0)
My experience is identical to yours. Old established site(s) that were well regarded by Google for years... and then hit for reasons that I am no closer to understanding now than I was back in April 2012 when Penguin struck.
Like you, my sites have never received a GWT message indicating what the issues might be, so we have to assume that changes to the Google algos are the root cause of the problem.
As far as I am aware, sites in this situation have to make changes that satisfy the algo and any changes should have an effect as soon as the pages are re-indexed. These sites DO NOT have to wait until the next Penguin update (if I understand correctly.) Reconsideration requests, disavowals etc are only for sites that get a message.
This "satisfy the latest algo" approach has had no effect on my sites... all the recommended actions from MC and John Mueller have had no effect at all.
I would not be too quick to dismiss the idea of anti affiliate bias. In my niche, every singe small to medium affiliate was wiped out around the same time that Google Hotels arrived and the travel sector was gifted to the big brand names.
Not one of those small to medium sites has ever come back... that's a group of about 20 something sites, all owned/operated by experienced, savvy web practioners with years of experience and not one of them has been able to come back.
I've posted on this subject a couple of times in hopes that someone would jump all over my commments as unfounded crud and give some reasons why.... but to date no-one has.
You will see similar comments from many, many people who are in the same situation where all their years of effort is being sacrificed at the alter of Google's profit and share price.