You MUST try the capsule hotels............they are sooooooooooocool! Most have tv/dvd aircon, and superb orthapaedic bed.
A couple of my friends went last year, hired a motorcycle, and stayed almost exclusively in them cos it was so much fun, and cheap too.
see: info@capsuleinn.com 
I was up for trying those, but a mate i am going with is not. He's a big chap, and looking at the photos he would not find them to his liking. Also there is the issue if i would fit, i'm 6ft4/5 ish (i really should check!) My feet stick out the end even on super king beds, so i doubt i would fit in them :-/
I'll take some details of them though for backups, this is my main choice:
http://www.sakura-hotel-ikebukuro.com/hotel_rates.phpWorks out at £40 a night, gets good reviews. My save capsual style hotels for Kyoto, as plan to go down there after a few days in Tokyo