I have no doubt that certain aspects of 'Penguin' involve penalisation. My experience has been confounded by the fact my main website currently has a manual penalty applied (for 'inorganic backlinks') but this was specific to certain keywords and only really affected the home page to a large degree. When Penguin hit pages that should rank naturally in reasonable positions without any backlinks at all (non competitive phrases and in tune with site theme very closely) disappeared into thin air. Maybe there are different degrees and it tries to discount things but I have no doubt in my case that a severe penalty is in place site-wide. I also see casual mentions of the things I would expect these pages to rank for on my Twitter feed outranking the page by far and this shouldn't be the case unless there is a penalty in place - not to that degree.
Furthermore some of my review pages that were naturally very popular and receive lots of natural backlinks were shoved into nowhere. Seems that Google mistakenly thought that some of these links were built by me or weren't giving any 'benefit of the doubt' given the overall link profile of the website. What that boils down to is a penalty, not a discounting of links. Some similar review pages which didn't get this kind of publicity rank much better and they have similar competition and search volume metrics and on-page elements are very similar.