I'm quite sure that I couldn't manage without Jorudan's train route detail website. Type in your starting and ending station and it tells you where to change, how long the ride will be, and how much it costs. Doesn't matter whether you're going across town or across the country--this is one great resource.
In English: http://www.jorudan.co.jp/english/norikae/e-norikeyin.html
In Japanese: http://www.jorudan.co.jp/norikae/norimap.html
Kuri-san, you can actually input romaji into the train-scheduler-thingy at yahoo.co.jp as well. It returns only Japanese but I suppose it is good for one's kanji learning?
http://transit.yahoo.co.jp/