The quantity and quality of public transport available in Japan is really amazing. It’s convenient and easy for locals as well as for tourists.
In cities you can use trains, buses, trams, monorails and taxis. 'Local' trains stop at all stations while 'rapid' trains make few stops and the ride is quicker. For convenience it’s better to use a Suica card (or any other of that type) valid on any kind of city transport. Even if you don’t have enough money on the card you can top up your card at any station with no problem. Taxis are a bit expensive, but in some cases they are very useful. For instance if you can't find easily find your hotel or another place.
Long distance travelling can be made on the famous ‘shinkansen’ bullet trains. There are also local trains, intercity buses, ships and planes.
In tourist towns travelling is eased by cable cars, tourist buses, cruise boats, rented bicycles or old-fashioned rickshaw!
Please, keep in mind that transport in Japan travels on the left side!
Picture 8 in actually a car of the Hankai tramway, but different sections of the rail are not in the middle of the streat and they have some "stations" like the one in this picture, so sometimes it does look like a train.