Japan is very accommodating to foreigners by offering discount airline fares as well as discount train tickets for those who have a foreign passport. However its good to keep in mind the above mentioned discount air and train ticket requires a visitors visa which us SOFA status members do not get. So its good for all those non military foreigners in Japan.
However All Nippon Airlines, a member of star alliance, has their own program called Experience Japan which offers any segment between two Japanese cities for 10,800 yen ($90 USD). The only requirement is you hold a foreign passport and have a ticket going to and from Japan.