When I went I saw Kagoshima, Hiroshima, Osaka, Nara, Kyoto, Kanazawa, Tokyo, and Hakodate. Didn't get to see Fukuoka, Okinawa, and Sapporo which I would like to see on a return visit. Osaka was my favorite actually, even more than Tokyo. It is so huge and seems more chaotic than Tokyo which surprised me, Tokyo seemed more clean and organized where Osaka seems a but more gritty and randomly assembled. In some places Tokyo is so polished and fashionable (Louis Vuitton, Gucci, Prada, etc are everywhere) it can feel almost European, especially walking in the low rise neighbourhoods around the Tokyo Tower but that is not the case in Osaka. Osaka also made a great base for short trips to Kyoto and Nara (note the quickest way to Nara isn't on JR). I would have liked to have spent about as much time in Osaka as Tokyo (including the short trips to Kyoto and Nara). I had Rail Pass Green tickets because of the sizable luggage we were carrying... trying to find a spot for luggage in the regular cars is often difficult... it seems they travel really light in Japan.
I can't wait to go to Japan again. I think next time the focus would be Okinawa (maybe R&R before heading home), Fukuoka, Osaka, Tokyo, and Sapporo (skiing if the season is right). The shinkansen is undergoing a three major expansions which we could see while we were there.