Citadines - A very long walk from the station and right next to the red-light, dangerous district of Tokyo, but easy to find and after a while, you'll probably discover that the most dangerous area of Tokyo isn't actually that dangerous at all when compared to other places around the world, even London.
The rooms are apartment-style, including a kitchen. The rooms are very clean, and sometimes include a TV which slides around the wall. This is probably some of the most modern hotel room lots you'll get, but keep in mind what I said about Japan's modernity in my other blog post.
If you prefer quieter areas, try Asakusa.
Asakusa Richmond Hotel's right next to a park with famous temples and shrines. It's also a short walk to a railway station, and from the shopping district of Asakusa, Tokyo.
Comfortable and spacious, has multiple baths. I think you can book them, but I'm not sure. This is similar to another place I stayed at in a totally different location, but at this other place, you could get a room with its own hot spring bath. It was very nice for relaxing.
The hotel is right next to downtown Kyoto, perfect for shopping. Or you can get on a train and travel to the more cultural outskirts. Kyoto has several large monasteries, some of which you can walk through.
Hankyu - Top-class and doesn't break the bank.
But if you're more traditional, try this:
It has a church!! HALFWAY UP THE BUILDING, ON THE 22ND FLOOR!!!
Yamaichi Bekkan - The room I had was at least the size of three normal tatami rooms put together. It had two bathrooms and two verandas, with one giant room being split in two by the traditional japanese sliding wall. Very nicely set out, though we did have a bit of an ant problem on the first night (don't know how they got in, but they were going for the light-coloured bedding and the light of the room, I think). Quite clean, good location next to port, the beach, the tourist attractions and the deer :D
By the way, I looked at the negative reviews - they don't really seem that justified, even when backed up by pictures taken by the reviewer. One says they had a dirty sink but honestly I saw nothing wrong with it! The small room mentioned was also the said room booked, and the same size as the room I had in a location after Osaka (admittedly small and disappointing for three people) but it's not representative of the hotel's quality. I also heard none of the aforementioned loudspeaker sounds, and besides, these are not the fault of the hotel anyway. Japan's full of cars that go around announcing things about the day such as how it is 'cleaning day'! Not sure what happened with the family that was unable to make contact with the place, that seemed a bit out-of-character of them. Anyway, it's a good hotel - check out the largest rooms they have if you're staying for a while.