Trains

Trains, trains and more trains . Not the only way to travel in Japan but definitely the most effecient and enjoyable. The JR pass if used correctly will be be worthwile, see the Shinkansen for a few ways to use it.

For timetables and prices I found Hyperdia to be highly reliable
For the big cities invest in an IC Card not only for travel for the buying train snacks. The JR Network covers the whole country (JR Central, JR West, JR East , JR Hokkaido, , JR Kyushu and and JR Shikoku)
IC Card is used for the private railays and Metro services in the bigger citis that will no be covered by your JR Pass

Train Etiquete
Eating and drinking are permitted on trains, however where the seat run down the side of the train ,its is not permitted. Where the seat run across the train , two or more abreast then it is considered to be permissable. On very busy trains in the big cities it is considered impolite. Dont eat food with over powering smell
City stations have lines on the platform for queuing to get on the train, usually not smaller or rural paltforms.
On the Metro lines take note that there are female only carriages , its is not for male partners.
Where you backpack at the front on crowded trains.
Mobile Phones- Dont take calls and turn your sound down