You can choose various kinds of modes of transportation in Japan. Comparing them from viewpoints of their cost, speed, and amenity, find suitable ways for you!
Airplanes
If you travel Japan for few days, airplanes are the best ways for you. Airplane services save your time, and according to circumstances, the cost of airplanes is cheaper that that of trains. Also, in many cases, there are bus or train services connecting every airport with nearby central area.
Railways
If you travel Japan for days, railway travel is the best way for you. Foreign tourists can buy "Japan Rail Pass", and if you purchase this pass, you can use almost all JR services including Shinkansen, limited expresses, local trains, buses, and ferries without fare for a certain period (more than 1 week).
Bus
The highway bus service is the most effective way for saving your travel cost. The cost of highway bus service is cheaper than other. Moreover, you can save your travel time by using overnight buses. Beside, the big bus service company, "WILLER TRAVEL" sell "Japan Bus Pass", and if you buy this ticket, you can use willer's bus network for 3 or 5 days without fare.
Other Ways