I've been looking at penalised sites since long before Panda and Penguin. The nature of the penalty i'm discussing is something that goes unmentioned in the community. Possibly because not many people see it unless they've noticed it on several sites. But as far as I can find, no one seems to have an understanding of it or answer to it. We often see people looking for help with their penalised site on BHW and I notice the homepage deindex and the inner page rankings but I don't see anyone mentioning this trend among penalised sites. I've only really noticed this on websites penalised for linkbuilding and i do not understand what exactly is at work. But I really hope we can crack this open through crowd-sourcing some solutions. On the sites i've worked on that have had a huge drop, but not total drop in rankings, i noticed that the homepage has been deindexed for the CORE keywords(this has been going on way before Penguin/Panda). Yet inner pages seem to be fine. What i notice is that even when a recovery of rankings is made, the homepage is STILL deindexed but only for core keywords. I don't understand this mechanism that is at work in the algorithm. I've not seen it discussed by Google or by experts and it is only commented on every so often in the community. For example, one of my penalised sites suffers from the Penguin update penalty. I've worked hard in recent months on its recovery and rankings have really begun to increase in the past two months. I assumed from my rank-tracking software that my homepage was being displayed in results but I recently manually checked and noticed that an inner page is ranking for core keywords. TL;DR Penalised sites often have their homepage deindexed but not their inner pages for core keywords. But there is no information about this.