Train Schedules and Route Planning
What I typically do is use Google Maps to figure out the greater scheme of things, and then switch over to the Shinkansen Timetable or the Train Route Finder to get details on the trains prior to reserving a ticket. Here's a breakdown of these services:
» Google Maps
A great option when trying to figure out how to get from A to B, wherever those two places might be. Simply use the »Directions« feature and the public transport option, here's an example using Google Maps to route you from Kagoshima-Chuo to Nagasaki. Being able to use this on the go is a big reason why you should rent a pocket wifi router.
» Shinkansen Timetable
When you need to find out what the Shinkansen options are when travelling from one major station to another, this is a great place to go. If you're using a Rail Pass, be sure to set the optional conditions to »Hikari, Sakura, Kodama and Tsubame« trains only, as you won't be able to use the rail pass on specific services such as the Nozomi ones.
» Train Route Finder
Basic but comprehensive service covering most train routes including non-Shinkansen ones. The user interface is rather cumbersome, though. Great when you want detailed info on specific routings.