Japanese rail lines can be lumped into three broad categories.

  1. National.  The big national railway in Japan is JR (Japan Rail), which used to be known as Japanese National Railways.  Although the JR lines are operated by several independent regional companies nowadays, JR's network connects just about every city in Japan with every other city in Japan.  JR operates the shinkansen or "bullet trains" as well as most of the high-speed limited express trains between major cities.
  2. Regional.  These lines connect different metropolitan areas, and often can create very confusing webs of track in the process. Regional railways in Japan include the gargantuan Kintetsu (Kinki Nippon Tetsudo) network, which connects Osaka, Nagoya, Nara, and Kyoto, and the slightly simpler Tobu line, which connects Tokyo and Nikko.
  3. Local.  Although local railways might span several cities, they never leave their given metropolitan area.  The Hankyu Railway, which runs between Osaka, Kobe, Kyoto, and points north of Osaka, is a good example.

The trains themselves also come in several classes:

  1. Bullet trains (always referred to as 新幹線 Shinkansen).  Shinkansen trains are literally the size of narrowbody airplanes, and riding one is very much like flying in an airplane, with comfortable seating, food and drink service, and all the perks.  They run on special tracks, separate from the main lines (to accommodate their extra-wide gauge), and reach speeds of around 150 miles per hour.  The Shinkansen network starts in Tokyo and radiates outward to Osaka, Hiroshima, and Fukuoka (the Tokaido-Sanyo line), Sendai and Aomori (the Tohoku line), Niigata (the Joetsu line), and Nagano (the Hokuriku line).  Shinkansen tickets are expensive, often moreso than equivalent airplane tickets, but the convenience factor more than makes up for this, and makes the trains popular with business travelers.
  2. Limited express (特急 tokkyu).  On JR and regional railways, a limited express train is a fast, expensive, cushy way to get from point A to point B.  Most people take the limited express because it is cheaper than the Shinkansen, or simply because the Shinkansen doesn't go where they want to go.  For the most part, the limited express is like a Shinkansen Lite: the major difference is that limited express trains are smaller and operate over lesser distances.
  3. Express or rapid service (急行 kyuko, 快速 kaisoku, or, on local lines, 特急 tokkyu).  These run on normal tracks and charge normal fares, but they skip minor stations.  JR, for the most part, has one class of rapid service, called kaisoku.  Private railways usually have a few levels of rapid service, with 快速急行 kaisoku-kyuko ("rapid express") being the fastest, followed by 急行 kyuko, 快速 kaisoku, and 準急 junkyu, which are usually glossed as "express," "rapid service," and "semi-express."  In addition, many local railways have "tokkyu" trains that run very quickly from one end of the line to the other without stopping in between.  If this sounds utterly confusing, that's because it is--usually, the only way to tell which train is fastest to your destination is to stare at the route map for a while, or ask a conductor.
  4. Local trains (各駅停車 kakueki-teisha on private lines, 普通 futsu on JR lines).  These stop at every station on the line.  They are mind-numbingly slow compared to other alternatives, but they are guaranteed to get you to your destination, and, especially in coastal areas, can offer incredible views of the local scenery.  Most subways and inner-city rail lines (such as the Yamanote in Tokyo) only offer local trains.

Although they may look very different on the outside, trains do not physically vary that much on the inside.  Local and express trains almost universally feature bench-like seats on either side of the car and wide standing room in the middle, to accommodate rush-hour crushes of people.  Limited express trains have forward and rear-facing seats with a narrow aisle in between: on JR's "new rapid service" trains, you can flip the seatback to change the way the seat faces, and on some JR limited express trains, the seats turn around automatically at the end of the line so that the train always seems to be facing forward even if it is actually facing backward.

Limited express trains tend to be the wackiest-looking and wackiest-sounding of all: the Nankai Railway's rapi:t train, which runs south of Osaka and looks like a prop out of a Rocketman movie, is a good example of this, as is the slick-looking JR Sandaabado or "Thunderbird."

Riding on JR tends to be cheaper than riding on private railways.  This is not a universal law, however: certain lines that operate older equipment charge much cheaper fares than JR's.  JR West (Osaka) is also more expensive than JR East (Tokyo), but keeps its stations better maintained, so I'm not really complaining.  Some private lines, most notably the monorails in Tokyo and Osaka, charge absolutely ridiculous fares, but get away with it because they are monorails.

Streetcars, which were the norm in Japanese cities before World War II, are now rare.  Hiroshima has a fairly large streetcar network, paradoxically enough, and there is also a tram line in southern Osaka that runs in the middle of the street.

Scamming the Japanese rail network is pretty damn easy if you know a few tricks.