A bit late for Keith, but I just wanted to put in a word for the ryokan I always stay in when I'm in Tokyo: Sawanoya
http://www.tctv.ne.jp/members/sawanoya/
It's a really friendly place run by a nice family, all japanese-style as you'd expect, and with free internet access in the reception area and broadband in the rooms (own laptop/cat5 cable needed).
It's in the Ueno area in the Yanaka area which, while walking around the streets there, really reminds you of what old tokyo used to be like.
I've stayed there 3 times now, and am staying there again in a week or so when I head back out to Japan