I'm going to have to say that I'm generally, but only _partially_ in agreement with your list of examples. When talking about "best designs", I would definitely (but respectfully) disagree with the inclusion of StackOverflow, and GitHub. Specifically:
StackOverflow
Issues: mind-boggling bad layout (poor visual hierarchy, no clear organizing principle); inconsistent typography; too many fonts; weak affordances for useful functionality (filtering/sorting replies); hard to tell obsolete or ancient replies from newer ones
GitHub
Issues: quasi-random screen layout; hard-to-discover functionality; mystery-meat navigation; low-level behavior/affordance inconsistencies. (Editorial aside: this looks like the side-effect--or result(!), of a slavish application of an agile feature development model to the UI design of an application.)
StackOverflow
GitHub