I know I mentioned them before in a previous thread, and a few people have said that they did not like them, but I really like the Khaosan Ninja in Tokyo.
Khaosan Ninja I found the staff to be awesome and really friendly/warm. The rooms were not that great, but to be honest, how much time do you want to be spending in your hostel room when travelling??!! They had a really nice lounge area and kitchenette. I would always recommend them.
A trip to Japan wouldn't be complete without a stay in a capsule hotel. I stayed at the one in Akihabara but I'm not sure if it is still there. It is quirky but enjoyable and like I said, an experience not to miss.
Capsule Hotel
When visiting Nara, I stayed in a town nearby called Oji. Here I stayed in a place called Guesthouse Yougendo. It is a traditional Japanese building with accommodation and a bar. It was run by an English guy from Bradford and was a top stay. When talking to him, he said that he had bands like Prodigy wanting to stay and Bloc party stay when they toured as it was a traditional Japanese house and close to Nara. Oji was also a nice little place too. Another bonus was that they sold Guinness in pints!!!
Guesthouse Yougendo
I used a hotel chain called Hotel Route Inn a couple of times. They are nice clean westernised hotels so you don't really get that Japanese feel. But, if you are stuck for somewhere to stay, they are quite good.
Hotel Route Inn
One of the places that I stayed in at Kyoto was called Guesthouse Bola Bola. It was a nice place to stay in another traditional Japanese house. The family that owned it were really friendly, and they also made their own information leaflets for guests to take. It was not in the centre of Kyoto but just outside, easily accessible by the train.
Guesthouse bola Bola
Probably my favourite place to stay was called Business Ryoken Sansui in Hiroshima. It was a standard Ryoken run by a Japanese lady who could hardly speak a word of English. What made this one of my favourite places to stay was just how friendly the land lady was. Every morning she would give us oranges and sometimes yoghurts and made every effort to communicate with us and give us any help we needed, a real gem.
Business Ryoken Sansui
Hope this helps anyone.