If this application included JR, then I would use it more often. However, it does not, which makes it plumb useless for the Tokyo Metropolitan area. You need to have both JR (and other private lines) shown, as well as subway. I could care less about routes, but you need all the rail systems.
Until some app comes out with them, Ill continue to use my trusty printed Tokyo Rail Map.
CDM Personal Mac Acct about Japan Subway Route Map (Tokyo Osaka Nagoya)