For those looking for accommodations in Japan, may I suggest:
http://travel.rakuten.com/
I use it all the time, it has a lot of the japan specific, smaller and independent hotels that normally have japanese only reservation pages but with a full english interface and reviews and ratings from the japanese side of the site which is quite popular.
I managed to get an onsen booking in Hakone during the busy new years season when pretty much everything that was english accessible otherwise was completely full.