Japan's railroads belong to JR (Japan Railways, a group of 6 nationwide companies) and other companies functioning in most megapolises. JR's service features renowned punctuality.
JR Shinkansen's most prestigious service is Japan's Bullet Train. It goes to Tokaido (Tokyo-Osaka), Sanyo (Fukuoka), Tohoku (Sendai) and Dzyoetsu (Niigata). Speed and comfort divide japan's trains into express (Hikari), semi-express (Kodama) and super express (Nozomi).
Ticket booking is not expensive but do it beforehand - around a month. The train fee depends on the distance and service option. In cities you can buy tickets for local lines in special slot machines at every station.
Anyone can use a 5-day youth ticket JR Seishun 18 (Juhachi) Kippu Ticket (JR seasonal discount ticket for local and rapid trains) during student vacation for about $120 (11,500 yens).
For more information see here.
Kids under 6 travel free, 6 to 11 - half-priced.
2 types of passes save on transport a lot - the nationwide Japan Rail Pass and Regional Railroad Passes only for regional lines.
The Japan Rail Pass is a JR railroad ticket for 7, 14 or 21 days also valid for 1st-class travel by Green Car. It allows unlimited use of JR trains including Shinkansen (without the super express named Nozomi) in a certain period plus all the other JR trains, buses and ferries. It'll save greatly if you take several rides (for example, to Tokyo, Kyoto and back).
For more information see here.
They have the same limitations as the JR Pass. To exchange a voucher for a pass you'll need all necessary stamps in your passport.
From Tokyo you can get to Tohoku (northeastern Honshu, including Akita, Sendai, Nagano, Nikko and its famous rugged national parks) by the JR-East Pass for all local JR East's 72 railway lines - 5 Shinkansen lines, the Narita Express (N'EX) from the Narita International Airport to downtown Tokyo, and most local trains. The passes are valid for 5, 10 or any 4 days a month.
The 2-type JR-West Rail Pass best fits travelers from the Kansai International Airport to the Kansai area, including the historic towns of Kyoto and Nara and the noisy hub of Osaka with its many sights.
For more information see here.
Land cruisers available in any major tourist center are cheaper though slower than trains. Priced higher than city buses, they can serve better for those in a hurry. These buses stick to the schedule right. Their tours are likely to be commented in Japanese.
Daily inter-city runs are served by comfortable buses of JR, Odakyu, Seibu, Keio, Tokyu and some other bus companies. Most buses provide convenient transfers with major railroad stations. Many run at night - rather luxurious with reclining seats, toilets, tea and blankets. Others operate by day, offering excellent views alongside.
See also Nihon Bus Association, JR Bus Network, 123bus
Planes connect all Japan's prefecture centers from over 90 airports for domestic and international airlines. Japan is reputed as a most travel-friendly country. Its major air companies are Japan Airlines (JAL), All Nippon Airlines (ANA) and Japan Air System (JAS). However the 1986 air industry reform gave rise to many new local companies. Haneda Airport serves domestic lines from Tokyo while Limousine Bus vehicles run between the Haneda and Narita airports.
The Yokoso (Welcome)/Visit Japan Fare available only overseas gives visitors special domestic discounts (apart from the high season) to 42 cities served by JAL and its 2 subsidiaries - JAL Express in Itami Airport (Osaka) and Japan TransOcean Air in Naha (Okinawa). Booking and ticketing are tied to a JAL international ticket and come before entering Japan. The Welcome to Japan Fare also offers cheaper domestic flights by JAL with the subsidiaries. This discounted fare however is not limited to JAL.
A similar Star Alliance Japan Airpass and Visit Japan Fare for overseas travelers are offered by All Nippon Airways.
See also Japan Airlines (JAL), All Nippon Airways (ANA)
So many tunnels and bridges make you forget Japan is an archipelago. An inter-island ferry is the best way to access the Sado island or just voyage the Inner Sea. A night ferry to Hokkaido is cheaper than a train. For ferry voyages 6-40 hours long almost irrespectively of distance, the 1st-class ticket costs 9-27K averaging out 14K yens, the 2nd-class 5-14K averaging out 7,5K yens. More info on its routes, schedules and prices is available at JNTO (Japan National Tourist Organization) offices.
For more information see here.