Usability 
Tokyo and Japan: If you are in Japan or plan to visit there check out the Norikae-Annai (Train Route Finder) from Jorudan (jorudan.co.jp/english). It's an all-inclusive trip planner that not only covers commuter and subway trains in Tokyo but also intercity rail, bus and air connections throughout Japan. For each trip, Jordan will list the fastest route as well as several alternates. For intercity trips over a few hours the first route will be via air, complete with local connections to and from airports. Train Route Finder is an iMode site but seems to work reasonably well with the mobile browsers of most Western phones.