Bus & Trains

JR East Japan Railway

Train and ticket info on all JR lines.
http://www.jreast.co.jp/e/index.html

Tokyo Metro

Metro and subway information in Tokyo.
http://www.tokyometro.jp/e/

Hyperdia Train Route Planner

Easy to use route planner for Japans train network. Including timetable, transit points and costs
http://www.hyperdia.com/

JR East Japan Railway

Train and Ticket guide for the western part of the JR network
http://www.westjr.co.jp/english/english/index.html

JR Bus Network Kanto

Timetables, fares and other information for the JR Bus Kanto long distance network
http://www.jrbuskanto.co.jp/mn/aetop.cfm

Hato Bus Tours

Bus tours of Tokyo
http://www.hatobus.co.jp/english/index.html