Locke's goal, it seems, is to turn our ordinary beliefs into a system of metaphysics... Berkeley's project is, as he famously put it, to "think with the learned, and speak with the vulgar." His metaphysical system, he is well aware, bears no resemblance whatsoever to common sense. Nevertheless, he claims, his system preserves the correctness of common sense within its own domain.
It's a nice distinction, and I'm with Berkeley at least in thinking that we shouldn't read too much into the platitudes of common sense. "Folk ontology", for example, strikes me as an oxymoron: the folk don't have anything to say about the questions that interest contemporary ontologists. Ordinary talk of 'existence' invokes the 'superficial', non-ontological sense of the word. I'm skeptical whether there is any sense to ontology at all, but even if there is (say we can make conceptual sense of the objective structure of reality), that sure isn't a domain the folk are concerned with in their everyday talk of how many chairs are in the room. (It would miss the point to answer, "None; there are only atoms arranged chair-wise." This is not a difference of any concern to the folk.)
I think we also need to be careful about how we seek to integrate "common sense" moral intuitions into our moral theory. The folk concepts of 'right' and 'wrong' again strike me as fairly superficial, and so not of great philosophical interest. Moral philosophers (of my stripe) are instead concerned with the most fundamental normative questions, e.g. about what we have most reason to do. To say it's intuitively "wrong" to push the fat guy in front of the trolley is neither here nor there. The vague intuitive idea being expressed here may correspond to any number of more precise claims (e.g. that it's a bad rule/decision procedure to allow killing innocents, or that we should censure someone for acting so) that are quite compatible with consequentialism. So, properly understood, I don't think consequentialism is really counter to common sense at all. It's orthogonal -- addressing a different, deeper, question.
So, accommodating the claims of commonsense is often less philosophically demanding than one might expect. Still, we shouldn't be too complacent. In particular, it is not enough to simply give an account on which the folk platitudes come out true, if this involves revising their meaning beyond recognition. One might think David Lewis guilty of this, for example, when he analyzes modality in terms of concrete spatio-temporal regions. Such regions just don't seem to be the right kind of thing to be that in virtue of which our ordinary modal claims are true. At least, this surely violates the folk understanding of what their modal talk is about. That's not an automatic disqualification -- I'm often sympathetic to philosophical revisionism -- but it is worth noting as a genuinely "counterintuitive" result. (Similar remarks may apply to Berkeley's phenomenalism.)