only reason I'm posting this is because my BF is the web designer and I know the owner
Bamboo House provides affordable furnished apartments, guesthouses, hostels, weekly apartments in tokyo!
BUT I have been to two of their establishments, The one place was REALLY nice (The one in Nishi-nippori) it had a rock garden and a really cute open room, the other one (hmmm I think it was also in Nishi Nippori... Maybe Nippori..) Wasn't as nice, but had a garden on the roof.
Since they have weekly rentals and daily rentals you'll find it cheaper then a hotel, and if you get one of the dorm room situations it's probably on par with the price of most hostels.
I know it's cheaper then Sakura House.