Bob,
since you have traveled to Japan so many times, can you give me some pointers. We are planning on going to celebrate our 15th wedding anniversary but have no idea where to get good rates or deals or anything.
I know you asked Bob, but I figured I would comment.
If you go to Tokyo, I highly recommend the "Park Hotel Tokyo" in Shiodome.
http://www.parkhoteltokyo.com/index.html
After staying several times at the old standard, the Keio Plaza Hotel, I changed to the Park Hotel and was pleasantly surprised. It was vastly more modern, well-situated (though not right in Shinjuku like Keio Plaza), it was cheaper, and overall I just thought it vastly better. One exception, Kyubei, the tiny sushi restaurant in the Keio Plaza hotel is considered one of the best in Tokyo (i.e. the world). It is definitely worth trying, though it is pricy.
Bob's recommendation for the station hotels is a good one, though I don't know if I would stay in one while on an anniversary. Toyoko Inn is a very good chain, at least for the single male traveler...they have an English website too.
http://www.toyoko-inn.com/eng/ I have not stayed in their Tokyo hotel, but I have all up and down Tohoku, and in Hakodate in Hokkaido -- they are very consistent. Clean, free internet, coin op laundry and small, but comfortable rooms. Very good for business travelers.
If you are adventurous and up for something traditional, Jodogahama Park Hotel in Iwate Prefecture (the boonies) is amazing. It had the most beautiful view I have ever seen in a hotel. It is built right on a cliff overlooking a beautiful bay with nothing but pine trees, rocks and the ocean. The food is amazing, fresh from the ocean (some of it still kicking...the sea urchin was still twitching, and the giant clam was still alive when the woman set it cooking). The bad news is that it is expensive...get an ocean view though! In English here:
http://www.japanhotel.net/data/hotel_information.asp?HotelID=879&area=MIYAKO_IWATE
I speak Japanese and I think I was one of the first foreigners they had staying there. You should be able to get by though.
It looked like this in my room:
You can see the cliffs in the distance. This was the meal...for one....it was brought to the room, as is traditional.
This is from the boat tour...I went on a fairly stormy day: