There is a saying that once you mastered the art of travelling on Japan's extensive railway network, no other networks will faze you anymore.
I cannot agree more. I believe that Japan is the MOST rail connected country in the world, and this is also one of the main things that I love about the country. One can go just about ANYWHERE in Japan, even the remotest part, on trains. Nevertheless, a warning to all first-timers to the country: it is extremely complicated and can get pretty confusing, EVEN IF you have the train maps on hand.
Just take the example of Tokyo. The JR (short for Japan Railways) Yamanote line is simple enough - it goes around in a circle and stops at major tourist sites, so some visitors play it safe by staying near the line and not go anywhere else which limits true exploration of the fabulous city. Add to it other JR East railways (including the famous Shinkansen) going to and from Tokyo to other parts of Japan. Add to it private rail networks like Odakyu, Keio, Tobu, Hanshin, etc which goes to other towns/cities where within these towns/cities they have their own smaller local train companies. And right smack in the middle of Tokyo which looks like a convoluted bunch of angry coloured worms is the Tokyo Metro underground subway line. Many a times I have boasted to Samurai T that I am a "Super-Navigator" because I have a very good sense of direction and seldom get lost. But Japan's rail networks crush me totally.
I lost count the number of times we got lost. not just in Tokyo but also in Osaka. Because of the crazy number of trains, some of the large train stations are a veritable labyrinth. The Shinjuku station in Tokyo, which hosts God knows how many lines from how many train companies as well as Tokyo Metro is a nightmare. There must be about 30 to 50 different exits in the station across different levels with hundreds of shops, eateries and large department stores to confuse you. I sincerely believe that it is possible to get lost there and never come out. In our most recent trip there, we stayed at Shinjuku for 3 days, and at the end, I could not say with any confidence that I would never get lost in that station again, because likely I still will! If you have to change trains in Shinjuku, only one word of advice: PRAY for guidance. :)
Seriously it can be intimidating to many, especially if you are rushing for time. But actually, getting lost is part of the fun of travelling on Japan's trains. The Japanese, while not fluent in English, will be happy to help point you in the right direction. The stations have clear signs and maps which include quite a fair bit of English and Kanji. Exits are clearly marked. (It is the SIZE that is the problem.) Always try to identify beforehand which exit number (14A, 15B?) is the nearest to your destination, like your hotel (they will usually tell you on their website). If you are trying to catch an hourly train out of Tokyo in a big station, for goodness sake, go early just in case you get lost. We did not plan carefully when we wanted to catch an early Odakyu train to Hakone from Shinjuku, and spent a lot of time trying to find the right station entrance and platform. We made the train with less than 3 MINUTES to spare. It was a very good lesson for us - to go early next time!
Bottomline is, do not get agitated and there is much that you will gain out of train travelling. The trains are always clean, and you are generally guaranteed seats on out of town trips. You get to appreciate the beautiful landscape of Japan (the open rice fields, soaring mountains, crystal clear rivers and scenic beachfronts), and you can also enjoy your breakfast/lunch/dinner bento sets during the journey. Some of the trains are so beautifully decorated they are like works of art. They are punctual to the dot, and you know exactly what time you will arrive at your destination based on their clockwork schedule.
Enjoy the ride.