Many people know of the exceptional value of a Japan Rail Pass, which allows tourists to ride the train systems in Japan for a set period without paying individual ticket prices. Unfortunately, the Rail Pass is only available to non-residents of Japan, so if you’re not a tourist, then you’re out of luck!
However, there are many other forms of special ticket or pass available. These tickets are all outlined here
Most notable is the Seishun Juhachi Kippu, which is seasonally available and offers five days of “norihodai travel” (as much as you want), limited only to non-reserved seating travel on local and rapid trains belonging to Japan Railways. That even includes some of the slower shinkansen (bullet trains), I believe.
If you are travelling in the Kansai area for a few days, the Surutto Kansai Ticket is one of the better rail passes available in Japan. One of its advantages is that it does not only cover the train and bus lines between cities, but also most city buses and subways inside the cities. The Surutto Kansai Two Day Ticket and Surutto Kansai Three Day Ticket are rail passes, providing unlimited usage of trains, subways and buses in the Kansai Region (around Osaka and Kyoto), with the prominent exception of JR trains.
The Aozora Free Pass is offered by JR Tokai, and it allows the holder one day of unlimited use of local trains in the Chubu area. The pass is only available on weekends and national holidays, but at (roughly) 2500 yen per ticket it can be a great deal if you are going “day trip distance” from the city. I personally use this ticket quite a bit while hiking in the mountains surrounding Nagoya.
For detailed timetable information which includes JR and other trains, and flight information, please see the Hyperdia or Jorudan Route Finder websites. This not only tells you the fastest and most convenient ways to travel, it also gives detailed fare information, and different travel options.
For those who prefer a voice on the phone, Japan Travel Phone is a nationwide telephone service for those in need of English language assistance and travel information. Dial 0088-22-4800 (toll-free outside Tokyo and Kyoto).
Service hours: 9:00 a.m. to 5:00 p.m.daily.
Photo: Wikipedia “SeriesE233 JR-East chuou” by Sui-setz (Public Domain) – Modified