I recently found a "cool tool" for planning travel in Japan. The site is in both Japanese and English and offers detailed information about rail and air travel from point A to point B.
The site is called "Hyperpedia Timetable" by Hitachi Information Systems, Ltd. and it starts here: http://www.hyperdia.com/
(Just click on English for that service).
I've used it for planning on train trips from a station near us on the Kashima Rinkai Tetsudo Ōarai-Kashima Line which runs from Kashima City to Mito City. I've printed out timetables for trains to and from Mito for our local station (specific to my needs and much easier to read than the tiny print of the pocket timetable they offer). We also used it a few weeks ago for planning out trip on the JR Joban Line from Mito City to Otsuko Station in Kita-Ibaraki (the north end of of our fair prefecture) where we saw an art exhibit I'll be posting about.
The only drawback I have found is that you have to input the exact station name, so you have to find that out ahead of time. Sometimes the name is all one word as well, so that "Kashima Jingu" is entered as "Kashimajingu". Otherwise, it's great and gives you full timetables, any train changes along the way, and all the fares for your trip. It also offers maps, hotel and rental car information. Very handy website.
I've been making lots of business trips of late to Mito, so I really like having this service. You can plan trips anywhere in Japan and even compare rail with air travel. Check it out.
Another handy service I've found for English speaking travelers is Japan Google maps in English (well, Romaji letters anyway): http://maps.j-talk.com/ and this one, called Diddlefinger, which lets you look up specific addresses in English or Japanese: http://diddlefinger.com/