Making your way around Japan can be quite an experience- for many reasons. On the whole, long distance travel can work out fairly expensive, but at least you can hope to be comfortable. The easiest but obviously most expensive way is to go by air- Tokyo’s Haneda Airport handles domestic flights that link it to cities across the country. Ferries too commute between islands, and you can book a cabin or travel economy class- which is communal, but great fun.
Surface transport is a pleasure to use in Japan- both trains as well as buses have a good network, and are fast, clean and reliable. They’re also rather expensive, but if you buy yourself a JR (Japan Rail) pass, you can save quite a bit; what’s more, JR also has a bus network of its own, on which the JR pass can be used. One experience you mustn’t miss (if you’re a train-travel buff), is a trip on the bullet trains, the Shinkansen. Amongst the fastest trains on earth, the Shinkansen connect major cities to the north and south of Tokyo, and are basically of three types, depending upon the number of stops they make the fastest, the Nozomi, makes the least stops and is the only one on which a JR pass isn’t valid.
Within cities, a good option is to hire a car- there are lots of rental companies around, and you can either ask for a chauffeur or drive yourself. The latter is increasingly becoming a popular choice amongst tourists.