Here I present you the useful Tokyo Train Map! This map is written in Japanese and feel free to download or print it for your own usage. The map will be very useful for people who wants to travel in Tokyo by train. Look at the complicity of the route, but the train system will bring you everywhere!
By the way, you can also use this useful site to check the available train services to go certain places in Japan. Just key in where you are from and the destination you want to go, and it will generate route for you. I used that to confirm my train route and it is really handy!