From city to city, you can fly on one of the services offered by Japanese Airlines, (JAL), or All Nippon Airlines (ANA), who both offer competing services frequently on all major routes. The famous bullet train (Shinkansen Super-Express) operates on most routes, and is not only spectacularly fast, it is also very efficient, and always on time.
Around the major cities, you can get around using either an underground, or on the tram networks.
You can hire a car to drive around Japan, but whatever you do, do not drive in the bigger cities, at times when the roads are not clogged, and jammed, the driving is so "daring" that it will intimidate you in seconds.
