Train is perhaps the best way to get around Japan. Rail network is extensive and covers most cities in Japan. Usually fast, frequent, comfortable, though a bit expensive. Carriages are generally clean. I have never seen a graffitised nor vandalised train in Japan. The amenity of trains is being improved, still occasionally you may feel their layouts tight. Some trains (especially old types) were designed according to the relatively small physique of Japanese people or planned to fill the need to put many people in a limited capacity. Japanese railway is also very reliable transport. Surely the most punctual in the world, and fairly safe. In the following Shinkansen system, there has never been a fatality in its more than thirty yearsf operation. The fare is not cheap, but Japan Rail Pass, much cheaper than the standards of the ordinal fare, is available to travelers from overseas. Long-distance services are covered by Japan Railway (JR). Once it was one national railway (JNR, Japan National Railway). In 1986 it was privatised due to its surprisingly hefty debt more than 20 trillion yen, and separated into six regional passenger rail companies and one freight rail company. The result is successful on the whole, going into black and improving the services. When traveling, you do not care about the border of these JR companies because trains and tickets go through different companies as they were before separted. Besides, there are other private railway companies. They usually operate trains between city and suburban areas; some of them extend 100 or 150 kilometers from Tokyo or Osaka to the sight-seeing spot outside city; for example, Tobu goes from Tokyo to Nikko, Odakyu to Hakone. Large cities also have subways under public management. Trams (streetcar) are not so common in Japan today because many of them have already abolished owing to traffic congestion. Still, several middle-sized cities have tram lines, Hakodate (Hokkaido), Hiroshima, Matsuyama, Kochi, Nagasaki, Kagoshima, and so on.
Shinkansen (High-speed bullet train)
You can ride on Shinkansen without reservation (though you might have to stand in passage if seats are occupied), and train schedule is fairly frequent. So you can take Shinkansen at any time like subway without taking troublesome steps, which is a great advantage for busy Japanese businessmen. Some passengers run up the stairs to the platform and jump into the train just three seconds before the door closes. Its scenery may be rather dull because everytime Shinkansen line comes to mountainous areas or even small hills, it goes straight into a long long tunnel to avoid curving, which is the obstacle to its high speed. You can hardly feel a sense of the train travel as a hobby or entertainment here. But anyway, Shinkansen plays very important role in Japan. Without this mass transit, densely-populated Tokaido megalopolis corridor will never function. There are three kinds of carriages; Green car (the first class), reserved regular car (the second class), and non-reserved regular car which does not require advanced booking (see Tickets).
All the Shinkansen trains are supplement payable. Japan Rail Pass holders do not have to pay it, though.
Kyushu Shinkansen from Hakata to Shin Yatsushiro is under construction, and will open in 2011. After that, they plan direct service from Shin Osaka to Kagoshima Chuo.
Most of them consist of the same three kinds of carriage as Shinkansen: Green car, reserved regular car and non-reserved regular car. Ekiben (The station box lunch) are usually available on board as well. It is a bit inconvenient that Shinkansen and other train services are completely separated because the rail gauge of Shinkansen and conventional railways is different. You may often have to change Shinkansen to a limited express at the junction if you extend your journey off the beaten track, although schedule is generally well organized and you have only to wait for several minutes at the connections.
They are supplement payable as well.
Express (kyuko)
Overnight trains (Yako ressya/ 'Blue train' )
Sleeper cars require as much as 6,000 yen or even more expensive supplement even in the case of B-class carriages whose amenity are not so different from much cheaper 'couchette cars' in Europe. Although new type cars separated into small compartments by each one or two passengers and equipped with a key lock are available by paying only B-class fare in some trains.
It is currently the most luxurious train in Japan, introduced in July 1999. It runs from Tokyo to Sapporo three days per week, about 1200 kilometers journey taking 17 hours. Carriges are all 'A-class' (first class) sleeper car without conveying standard B-class cars. The most delux car consists of only four rooms, which gives large and comfortable space to passengers. It also has a restaurant car which provides French or Japanese dinner, shower rooms and a observation lounge.
It runs along the coast line along Japan Sea about 1500 kilometers for 21 hours, three services per week (runs every day during the vacation season). It is named after the beautiful sunset at Japan Sea, although I heard once that the implication of the word 'twilight' is actually negative rather than positive (I am not so sure, is it true?). Anyway, its 'A-class' sleeper car has only five large luxurious compartments per carriage, whose additional fare is about 17,000 to 25,000 yen. This train also conveys one good restaurant car (though expensive) and another comfortable salon carriage.
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Shinkansen is famous for its high speed; actually it is not only fast, but very convenient and efficient. It is surely the busiest railway (in terms of intercity passenger transport) in the world. For example, when you go from Tokyo to Kyoto or Osaka, you don't have to care for time at all. Shinkansen trains departs every 5 to 15 minutes even in Sunday morning. 
On the train, usually attendants who sell you Ekiben (The station box lunch) and other snacks come frequently; and in many times the cafeteria car is conveyed. Ekiben is also
sold at many stations.
'Toki' goes from Tokyo to Nigata, 'Tanigawa' ends at Echigo-Yuzawa or Takasaki on the way. Almost all the middle part of this line going through the mountain ranges in the center of Honshu Island consists of tunnels and not different from a subway at all. In winter, the climate of northern and southern side of that mountain ranges are usually quite different owing to the barrier of high mountains. Southern side is usually sunny and little snow, but northern district is always covered with clouds and often snows quite heavily in winter. So cloudless sky with no snow may suddenly turn into dark sky with one meter's snowfall after Shinkansen rushes through long tunnels in just ten or twenty minutes. There are many large skiing grounds along Joetsu Shinkansen, very popular destination for people in Tokyo. A branch line, Nagano Shinkansen, goes from Takasaki to Nagano, and 'Asama' connects Tokyo and Nagano.
The limited express service covers most cities in Japan. As the topography of Japan is quite mountainous, they are not so fast (Maximum 130 km/h aside from few exceptions) but most of them provides fairly frequent services. With this, you can usually travel about 90 kilometers' journey per hour (60 or 70 km in the less important, low-grade line). 
They are generally not very recommendable because the additional fare is high despite their poor amenity and slow speed. Now that much faster Shinkansen and air services as well as cheaper overnight highway bus become very common, overnight trains are not very useful measure to travel, at least in a practical sense. 
