I am typing this on the flight back with lots of great memories. We spent a lot of time travelling on the Shinkansen and local train and subway networks in Japan so i thought i would detail some of our experiences.
As i already mentioned in my previous entry, the Japan Rail Pass from JR offers excellent value. If you expect to make use of the JR lines then you should check to see if its worth buying. If your going to take any Shinkansen over an hour or so in length the pass will likley be worth it just for the one trip.
Train stations in Japan are usually large affairs and often are part of bigger complexes of shopping malls, restaurants etc. They will likley be on multiple levels with many exits separated by long walks. They are usually busy as the rail network provides a big portion of Japans transport network but are generally well signed in English.
You will also get different lines operated by other rail operators and subways integrated into the same station, not all of which would be applicable to free travel with the rail pass. However local trains are cheap and frequent.
Ticket machines for local trains are located close to the barriers of the lines they are for. They allow you to select a ticket price and quantity on the screen. They accept 1000¥ notes and coins. A large map usually located above the machines will show the stations and the cost from where you are to that station. Unfortunately many of these signs show the price in numbers but the name of the station and line in Japanese characters so sometimes you will need to ask at the ticket desk where they will either issue a ticket for you or tell you the cost of the ticket you need to buy.
The tickets are a small postage sized card that is fed into the barrier, dont worry that the barrier looks like it is designed for different sized tickets, they are but accept both. Just feed it in and the gate will open popping out the ticket on the other side. Tickets are retained by the machine on your destination. Tickets issued at the manned windows are the larger size ones.
If your using the rail pass you dont use the automated barriers. There is usually a guard located at the side of the gates who you simply show your pass to. The JR Rail Passes are very common. The officer will normally just wave you through without needing to read the entire pass. Some barriers appear to be unmanned, but you will either find another manned barrier close by in the station or possibly a glazed passageway just next to the barriers where one or two officers are there to help with passes and other ticket issues.
Toilets in stations are generally located after the ticket gates, if you have a rail pass you can simply pass through the gates to use the toilet and then just walk back. With stations that have adjoining malls and restaurants just walking beyond the station area will often reveal public toilets.
Subways operate in exactly the same way as trains, they use the same mapping method, ticketing machines and barriers so if you can use the trains you can use the subway too.
Switching between lines and subways can sometimes be confusing especially if your switching between operators as they are often in different locations in the station. Sometimes they can even be next door meaning you might need to walk out of the station to find the subway for example.
Stations can get busy at peak times, Shinjuku for example is busy most of the time and gets crazy at peak times. If you dont like crowds then, well you probably came to the wrong country! If you know where you want to go during the busy times that's fine but if you dont know what train to get, or not sure what ticket you need then its probably best to wait until the crowd dies down.
We found the rail and subways an excellent way to travel Japan. Though in summer you can end up being baked on the platform sometimes!