Bus and coach travel offers the cheapest option for long-distance travel within Japan. Moreover, they are clean, spacious, and, as with everything in Japan, punctual. For longer journeys many companies offer an overnight service.
There are many bus companies operating in Japan—some national, some regional. Willer Express and JR Bus are the two main operators for inter-regional travel, the former also offering the Japan Bus Pass which is similar to the Japan Rail Pass in that is it only available to non-Japanese passport holders. ¥10,000 = $90 (FX rate updated daily).
Whether you opt for the multi-day pass or to purchase individual tickets, the highway buses (especially factoring in the saving of accommodation if you travel overnight) presents an extremely economical way to see the country. A one-way ticket between Tokyo and Kyoto, for instance, can be purchased for as little as ¥3,100 ($28), compared with ¥13,500 ($121) on the Shinkansen.
For visitors looking for organized tours, there is also Hato Bus (familiar to all Japanese due to their bright yellow coaches) which offers tour packages (in multiple languages) in and around Tokyo.