This is probably useful for anyone in the Tokyo/Kanagawa area: I found a huge train line chart online that shows all/most of the lines in Tokyo and Kanagawa. Normally no single chart shows all lines because they are owned by different companies, and it's even harder to find a good map in English, so I'm quite happy with this one. It's fan-made so it's not 100% reliable, but from what I can tell everything in there is absoutely correct. So useful!
http://www.mukiryoku.com/Tokyo_suburban.jpg
Today I was supposed to go look for a new apartment, but I went to bed late last night and woke up at 1PM. Then I somehow got caught up in reading Wikipedia's articles about trains, which lead to me finding aforementioned chart. After that I found out that Microsoft Train Simulator actually includes the Odakyu line which I have to take to get to Tokyo, so I installed that and gave it a try. Driving trains is easy, except when you're on a tight schedule, and in Japan every second counts. Literally. Leave one second too late and you'll be too late at the next stop.
MS TrainSim's graphics seriously suck, though, and it's quite difficult to recognize any station on the Odakyu line except Shinjuku. I looked around a bit for better trainsims but it seems difficult to.. 'acquire' in a fast and internetty kind of way, so I gave up. I did find a great flash applet that takes a quite different approach to train simulation. Take a look at it here. Why bother to design a 3d world if you can just take a movie of the actual train driving the route, right? Can't be more detailed than that :D