I'm certain Penguin is certainly majorly about backlinks (at least that's one of the signals that affected me). I have two popular sites. One is popular because of a software that I have been releasing for the last 5 years and had naturally gathered a lot of links from all sorts of sites/directories. Today if I use google to search for link:site it shows only 6 pages of links. Whereas WMT says 384,800 backlinks. So essentially WMT is able to give me an insight of the actual links and Google just tells me the ones that count. This leads me to believe that a lot of directories, low-quality sites were totally annihilated and/or their outgoing links devalued. I have seen this for both my sites of which one was affected by Penguin.
Is there any chance Google search would not show all the backlinks unlike WMT (which shows all backlinks)? I guess Penguin made those links disappear from the search page.