I've only been to Tokyo, we stayed at the Conrad which I highly recommend. It's conveniently located in the Shidome area, right next to Ginza and Tsukiji. Some quick links below, more if you use the 'SEARCH' function and specifically in the TimeOut forum section:
An amazing dinner and entertainment at Waentei-Kikko (the chef owner Fukui Kodai is one of the rare instructors and master of the traditional Japanese instrument, the Tsu-garu Shamisen. Staff and owner were so wonderful as was the meal:
timeout.watchprosite.com
fellow Purist 'cen@jkt' trip to Japan:
timeout.watchprosite.com
Had some of the best sushi at Kyubey in Ginza and the sushi breakfast at Sushi Dai inside Tsukiji Market was well worth the wait:
www.network54.com
PuristS on Tour Tokyo:
timeout.watchprosite.com
Recent recommendation for accommodations:
timeout.watchprosite.com
ED-209's review on Din Tai Fung in Tokyo:
www.network54.com
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Tea Ceremony at Hamarikyu Garden:
www.network54.com
We did a city tour that is half day (they offer full day as well), it was a good way to check out some of the major landmarks of the city (the Meiji Shrine, Tokyo Tower, Imperial Castle, Roppongi, and Akihabara) We also took the Waterbus that is at the Park next to the Conrad down to the Asakusa, along the way it passes over several colorful bridges.

This message has been edited by DRMW on 2013-05-19 15:46:55