Riding Trains & Subways
There are many different types of trains but they can be grouped into two basic categories. Normal trains run just about everywhere, go at a modest speed, and are basically what people take the vast majority of the time. A local train will stop at every station along its line but some lines also have rapid, express, or limited express trains which only stop at the larger stations (and therefor go a bit faster). While normal trains are great for traveling to a lot of places, if you're going somewhere really far away you're going to want one of Japan’s famous shinkansen (bullet trains). They cost extra to ride and only stop at a handful of stations but they can cover long distances in no time. But no matter what type of train you ride, you can be sure that it will be clean, safe, and highly punctual (while delays can happen, they’re rare and usually very brief).
Naturally, you can't travel between any two points on only a single train. Often you'll have to switch trains mid trip, possibly several times. Fortunately, you don't need to buy separate tickets for every train as most of Japan's train systems are run by the JR (Japan Rail Company). Because of this, prices are based on the distance between your starting and ending point, not how many trains you need to take to get there. So long as you don’t leave the station, your route doesn’t matter, just the distance.
Train stations typically have a bank of automated ticket machines (most of which have a button to switch the interface to English) where you select the ticket you want and put in your money. Tickets are sold by price, not by location. To find out how expensive a ticket you need to reach your destination you can check the big map that every station has near the ticket machines, find your destination, and read the listed price. Unfortunately, only the bigger stations have an English board but you can look up the price ahead of time on the extremely useful Hyperdia search engine, which is also great for finding routes, checking train schedules, and the like. Be sure to bookmark it you’re planning to visit Japan as you’ll likely be using it a lot.
If you still don’t know how expensive of a ticket to buy, or the machine won’t let you buy one for the correct amount (this is common if you’re traveling a long distance), all stations have fare changing machines near their exit gates. Simply put in your ticket and then insert the amount of money shown and you’ll get a new ticket which can be used to exit the station. Note that these machines won’t refund your money if the ticket you bought was too expensive so when in doubt buy the cheapest ticket you can and use the machine at your destination to pay the difference.
So anyway, you buy a ticket, stick it in a slot on the gate that leads deeper into the station, and grab your ticket when it comes out the other end. NEVER FORGET YOUR TICKET since you'll need to stick it in another gate at your destination in order to leave the station (when leaving you don't get the ticket back, unless you got a round trip ticket, day pass, or the like). It's worth noting that really old stations might have an employee punching people's tickets instead of an automated gate.
So, what are the costs? Depends. If you're just going one or two stops and they're all close together a ticket might just cost 100 – 200 Yen. Traveling long distances, however, can easily cost several thousand Yen or more. Then there's extra fees. For example, many trains have Green Cars. They're special cars with two floors and nicer seats, plus you get a reserved seat (which regular cars lack). Unsurprisingly, if you want to ride in a Green Car you need to buy an extra Green Car ticket, which are available from special machines found on the train platforms. Also, if your trip plan involves riding on a shinkansen or some limited express trains you'll need to purchase additional tickets for them along with your regular ticket (which are either put through the ticket gate at the same time as your regular ticket or shown to the conductor onboard the train, depending on the station). Look for special shinkansen ticket machines near the normal ones or ask the person in the ticket booth if you’re stuck. Shinkansen tickets are also based on distance traveled and can easily run several thousand yen depending on how far you’re going. So a several hour shinkansen ride might cost you 4000-5000 yen for your regular ticket plus an additional 3000-4000 for the shinkansen ticket, and that's just one way (sometimes, discounted round trip tickets are available). Note that you can save some money by getting a ticket that doesn’t include a reserved seat, though there’s always the danger you’ll be stuck standing for part or even all of the trip. I never buy reserved seats and I’ve yet to see a shinkansen so full that I couldn’t find an empty seat, but it could happen.
If you're planning to visit Japan and aren’t just going to stay in a single city for the duration of your trip, you may want to order a Japan Rail Pass, which gives you unlimited rides on most trains, a few busses, and one ferry for free during a span of one to several weeks. Instead of buying tickets, just show your pass to the person in the ticket booth and he’ll let you through. Note that, unless you pay extra, the pass is only good for unreserved seats. Depending on how long you plan on staying, a Japan Rail Pass could costs up to several hundred dollars but it’ll quickly pay for itself if start riding the shinkansen (a round trip between Tokyo and Kyoto, for example, costs a couple of hundred dollars on its own).
Subways (the best way to get around much of Tokyo and several other major cities) are similar to trains, except that they only cover single cities (usually far more extensively than the local trains), never run more than a few dollars for a ticket, and don’t accept the Japan Rail Pass.
When riding a train, grab a seat if you can but be prepared to stand. I've been on trains that were nearly empty and trains where people were literally jammed in like sardines (which is why you really don't want to travel the wrong direction during the morning rush).
It's considered rude to talk on the phone while on a train and there are lots of signs reminding people to put their cellphones on vibrate (or 'manner mode' as it’s called in Japan). Eating on the train is also considered rude (unless you’re in a Green Car or on an Shinkansen) but people occasionally do it anyway. In addition, most cars have several seats at the end that are set aside for people with injuries, pregnant women, people with babies, etc. However, if there aren't any people like that in the car said seats are up for grabs and, like the rest of the non-reserved seating on a train, seats are on a first come first serve basis. If you can't get a seat, find a place to stand, hold onto a bar or one of the rings hanging from the ceiling so you don't fall over if the train jerks unexpectedly, and try to grab a seat when someone nearby gets off.
Common train pastimes include cellphone e-mail, MP3 players, books and magazines, portable video game systems, and sleeping (I often wonder how many people accidently sleep through their stop) so if you're going to be riding the trains a lot get into a habit of bringing something to keep you occupied, though make sure to watch the scenery during your first trip on any given route, as you never know what you might see.
Oh, one last thing. While some trains announce upcoming stops in English and Japanese, many don't so pay close attention to announcements (listen for place names), the route map or electric display over many doors, and/or the place name signs outside the train at the stations (which are always in both English and Japanese) to figure out where you are.