Train
Ask for a jikokuhyô (timetable) for listings of times for all trains, ferries, night buses, discounts, etc. All the schools have the comprehensive timetable but you can buy smaller pocket-size versions at all bookstores. JTB has a bilingual version. The sooner you learn how to use this book the better. The different types of train are: futsû, kyûkô, kaisoku, tokkyû, and shinkansen, in ascending order of speed and price. Buy tickets from vending machines, "Green Windows", or on the train. There are literally hundreds of special tickets (for example shûyûken - excursion tickets) so don't be afraid to ask. Call the JNTO. Some examples follow (please note that some dates may for tickets may have changed and prices have most likely increased) :
SEISHUN JÛ-HACHI KIPPU: Purchase at any station during school holidays for five days of unlimited travel anywhere in Japan using futsû, kyûkô and kaisoku trains. Use the Japan Railways (JR) timetable (jikokuhyô) to plan your schedule or ask someone at the station JR information counter to make a schedule for you. (11,500)
SHINKANSEN FURÎ KIPPU (Weekend Free Ticket): Jiyû seki (unreserved seats) or pay an extra 500 for a shitei seki (reserved seat). Unlimited use of the shinkansen within a region (either East or West) on Saturday and Sunday. (16,000)
JR FURÎ KIPPU: Various kinds based on the destination and length of stay. For instance, for Hokkaidô it is best to purchase a region pass (dônan, dôtô, dôhoku dô) which will give you unlimited use of all JR modes of transportation within that region for seven days at a cost of 20,000-30,000. It is free to reserve a seat.
WAIDO: Again prices vary. Tokkyû and shinkansen are excluded and you may not reserve seats, sleepers or Green Cars (first class). Get on and off as much as you like and there is unlimited use of trains in designated regions.
NYÛ WAIDO: Same as above but no return ticket.
R KIPPU: Return on any train within six days with a reserved seat.
S KIPPU: Same as above except with a four-day limit and with standard seats.
R KIPPU 4: Two return tickets, unlimited duration (within three months). Therefore go two times or bring a friend.
S KIPPU 4: Same as above but with standard seats.
YAKÔ (NIGHT) TRAIN: The trains run along the Tohoku main line. Travel at night with a basic sleeper one way to Sapporo. (About 30,000)
GO GO FURÎ KIPPU: Available up until August 30th. Non-reserved seats for three days - Friday to Sunday or Saturday to Monday or any three days from around August 6th to 16th. Good for all JR East lines including Tôhoku, Yamagata, Akita, Jôetsu, and Nagano Shinkansen lines. (25,000)
KYÔ-NO-NATSU YÛYÛ KIPPU (A ticket to enjoy summer in Kyôto): Return by shinkansen (except nozomi) to Tôkyô. The ticket is good for four days and if purchased in Tôkyô it will include a "Kyôto Kankô Jôshaken" which allows unlimited use of Kyôto's subway and bus system for two days. Pass cannot be used certain dates and ends in September. (27,000)
KYÛSHU NORIHÔDAI KIPPU (Kyûshu Free Pass): You must buy this ticket in Kyûshu. Available up until some time in September. Use on all train lines in the prefecture except shinkansen and expresses. (One day 3,000, two day 5,000)
SEKAI-ISAN GURUTTO KIPPU (A pass to visit World Heritage in Nara): Must buy before November 23rd at major Kintetsu train stations. Good for any two days (Saturdays, Sundays, and National Holidays) to September 23rd, and any two days October 1st to November 24th. May also purchase a joint Nara Kôtsû Bus pass for one day (leaves from Kintetsu Nara Station 9am-4pm to the six UNESCO sites). A joint pass is 1,640 from Kintetsu Namba station (Kyôto), 1,740 from Kintetsu Kyôto station, and 4,440 from Kintetsu Nara station.
SHÛMATSU NORIHÔDAI KIPPU (Weekend Free Pass): Buy at JR stations in Shikoku. Good for one day on weekends, national holidays and from December 31st to January 3rd. Use all train lines, or rent a car at a significant discount at fourteen train stations including Takamatsu, Matsuyama and Tokushima. (10,000)