This post will only make sense to people living in Japan.
Just found a really nice feature on my cellphone using Yahoo Japan's train navigator 路線情報 (rosen jouhou = route infomation ). It allows you to enter your stations of departure and arrival, and it suggests a few routes and upcoming train times. The information is pretty comprehensive.
Of course, comprehensive information is a double-edged sword in that it's difficult to read. It's enough of a pain in one's own language, let alone Japanese! I just discovered today that there is a small text link at the top of a suggested route, 停車駅一覧 (teisha eki ichiran = list of stops). Clicking this gives you a simple top-to-bottom list of the stations your current train will stop at, followed by a list of the stations the subsequent train in your route will stop at, followed by the next list if there is another train in your route, and so on.
One really cool thing I found was a little train icon with blinking red text that says 今ココ！ (ima koko! = currently here!), beside the name of the station you're currently at, or will soon stop at. I'm still not sure if that is given based on the current time (since the route info is specified right down to which train at what time) or on your phone's GPS information. Next time I've got some serious time on my hands (yeah right!) I'll try an experiment whereby I will just get off at a station and wait for the next train and see if that "currently here" indicator readjusts itself based on where I am, or if it just advances on its own according to the time. I'm pretty sure it's based on GPS, since it would be inaccurate to tell someone they are some place they are not.