I'm not sure what you mean by guest houses- but If by a 'bed and breakfast', Im sure there are some, but are probably just as expensive as a hotel.
Your best bet is a hostel. Its like a dormitory with bunk beds and a shared bathroom. This sounds kinda lame, but it's actually a good experience.
Try the Sakura Hostel in Asakusa if you want to visit Tokyo- and I'm sure there are others which are equally as cheap and accomodating.
Hostel are usually around 2500 yen... or like $30 USD
Click here for Sakura Hostel website