One of the best transportation deals available to travelers to Japan is the JR Rail Pass which gives you unlimited train rides on almost all JR Trains including the Shinkansen Bullet Trains. This one pass can save you hundreds of dollars and pays for itself with just a round trip between Tokyo and Kyoto. This pass is only available outside Japan so you will need to purchase it before you arrive. For more information please see http://www.japanrailpass.net/ and when you are ready to purchase your JR Rail Pass please visit ACP Rail.
Many airlines are also offering discounts,
For not resident in Japan;
JAL and ANA offer several passes that have to be purchased in your country. For more information please see below:
The "One World Yokoso-Welcome to Japan Fare"
The "Star Alliance Japan Air pass"
Finally but not last; the Low-coast Airlines offer very attractive prices. Here are the most popular low-cost airlines in Japan:
Air Asia Japan