This is pretty cool, absolutely mind-boggling to look at those long reference lists. There are a few more which I know but not mentioned yet and some I feel are missing some interesting details. And anyone who spot errors please correct me so as not to spread wrong information.
I recall more references some of which kj1980 mentioned in the ep threads, MakubeX2 also mentioned a few including the Ponytail references and one of a game poster, someone noticed that Kagami was reading Toki wo Kakeru Shoujo, Kaoru Chujo verified that the smoking middle age man is Ishihara Tetsuya, and Level E has a very good list on his forum. Seriously there are a lot of references!