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Usually for sale to visitors only before they come to Japan, Japan Rail's JR Pass is to be made available for sale within Japan from March 2017.

Since the introduction of train travel, the idea of luxury dining to the clickety clack sound of the train tracks have held allure and glamour for many travelers.  While Europe has the Orient Express, Kyoto's north coast now has a Japanese version, the Kyoto Tango Railway's Matsu train. Named after the pine trees that line the shore at Amanohashidate, it offers luxury dining in polished wood carriages, and spectacular views of the Japan Sea on one side and green mountains on the other. 

JR Tokyo Wide Pass gives you 3 days unlimited travel on JR trains in Tokyo and 10 neighboring prefectures for only ¥10,000
In Matsuyama, be sure to ride the groaning 1950s trams and the puffing Botchan Train. Travel in retro style, if not the greatest comfort.
With Ginza, Yurakucho, and Tokyo Station to the south and Akihabara looming to the north, Kanda might seem merely a place to change trains. Not the case - just look at all you would miss!
Kansai Airport to Nara and beyond by train or bus?  An insider guide rating the different options based on speed, convenience, frequency and value.
The heart of Osaka's bustling Namba district, Kansai Airport, great shopping and more are all accessible via the Nankai Line.