I give a big second to the suggestion of seeing the Tokyu Hands store and Takashamaya. The Takishimiya is very nice and the Tokyu Hands is one of the few stores where I actually buy things. I think there is a food area in that Takashamaya, if so definately check it out. One of the more unusual things about the Japanese department stores are their areas where they sell prepared foods.

Also since it is December, try to get to the flagship Mitsukoshi store in Nihombashi. It is almost surreal. There is a large central atrium with a giant statue in it. When I was there in mid December last year there was an organ set up with people singing Christmas Carols, in English, in the artrium. The food area in the basement is incredible. I got to try a really nice tea and bought some of the tea leaves to bring back.

Also, December is the heart of fugu season. If you are interested in the famous Japanese toxic fish, Kozue one of the restaurants in the Park Hyatt serves a very enjoyable fugu course dinner. Ive always suspected they dont have as much toxin left in the fish there as some other places Ive had it but I have had it three times there and really enjoyed it each time. The view from the restaurant is spectacular.