Whether new to Japan or not, the train system can be daunting. Especially in the big cities there area stunning variety of lines that must be sorted through, and if you are lucky different routes to choose from. In the smaller locations there may only be one line, but it only comes once or twice an hour. If you are not on the ball with everything you could end up utterly lost in the metropolis, sitting on a bench for hours, or worse missing your train entirely.
How do you get route information in English in Japan? I personally use Jorudan Route finder, but you can also use Hyperdia. They will give you routes, times, and even the cost. They will even suggest alternative routes for you!
Both sites are Johnny on the spot with JR and city lines, shinkansen, and to lesser extent are accurate for private lines as well. Both offer an iphone app of some variety, though I believe both are in Japanese. For a list of these and other useful iPhone applications for living in Japan see this article.