The wife and I have moved to our hotel at Ikebukuro, called the b ikebukuro, courtesy of Wotif.com. I was told that the b chain of hotels (there are several) were some of the earliest hotels listed under Tokyo hotels on Wotif's site.
It is not the largest room in the world but it is functional. I love the location, being just 3 minutes walk from Ikebukuro station (get out the East exit, turn left, see the BIC Camera store and walk down the street). It is in the heart of a city centre so food and entertainment are all nearby. Ikebukuro station is just a few stops from Shinjuku and Shibuya via the Yamanote line too.
The toilet is a little small but everything is there. The showers are like the bridge of the USS Enterprise: three different shower heads for your showering needs, a little complicated but you'll figure it out.
I also appreciate the laundry room where you can wash your clothes with the coin-operated washing machine and dryer. Pay TV is a 1000¥ a night: you buy a card from the machine in the corridor, stick the card into the TV slot, and voila, pay tv.
Oh yes, and there is free internet in the room. That rocks.
Here is a little video tour of our room at the b ikebukuro: