Train travel in Japan is probably one of the best in the world: very clean, modern, efficient, comfortable and very punctual .  

There are basically three levels of rail service for JR trains: shinkansen, limited express and local.  One of the best known rail services in the world is the high-speed Shinkansen or “Bullet Train,” which has scheduled service between most major cities including Niigata, Tokyo, Kyoto, Osaka, Hiroshima and Hakata.  Limited Express trains offer less expensive, long-distance service to cities not served by the Shinkansen on major JR routes.  Local and Rapid trains, as the name implies, provide shorter commuter service within urban areas and to smaller towns.

JR trains have two classes of service: ordinary class and first-class or “green car” service.  First class cars are identified by a green clover symbol next to the entrance door.  Green car service is considerably more expensive but more comfortable and less crowded. One other difference from the U.S. is that smoking is still allowed in some rail cars.  If you board one you will know it, but just move to another car if it bothers you.   

Bullet trains that accept the JR Pass have both reserved and non-reserved seating.  Check the sign boards, which are posted in both English and Japanese, to determine which cars are non-reserved.  The location of each car number is listed on the platform, so that you can make a line at the appropriate spot.  For a non-reserved train, arrive early to maximize your chance of obtaining seating.  Even for reserved seating, arrive 5 minutes in advance so that you have sufficient time to board.  The trains depart promptly.
Rail travel in Japan is relatively easy for foreign visitors since most stations have signs and schedule boards in English as well as Japanese. However, be prepared to handle your own luggage since there are no porters or carts at railway stations.  Travelers who can not handle their own luggage are advised to hire a guide to help them.  Each bullet train car has a section at one end of the car where large luggage can be slid behind the first row of seating for storage.  There are also large overhead racks, which can accommodate small and medium sized bags.

One bit of caution: train fares in Japan are very expensive compared to Europe and other western countries.  If you’re planning on taking the train frequently (or even if you only plan on one or two inter-city journeys), a JR rail pass may be a wise decision. JR passes are available for 7, 14 or 21 consecutive days of unlimited travel on the national JR network. (Travel on lines that are operated by private rail companies, metropolitan subways, monorails and tramways are not covered on a rail pass.)  Also, rail passes can only be purchased outside of Japan. Once in Japan, you take the voucher they gave you to an office in the train station and they will exchange it for the actual pass.  When you do so, you will have to decide what day to start the travel - they stamp it on the pass. You will also have to show your passport. (According to the fine print you are supposed to have your passport available whenever travelling on the pass. It isn't valid for Japanese citizens.) But once you have the pass, just show it at the entrance gates and off you go. (Hint: when you get the actual pass ask for a copy of the English language Shinkensen schedule, if you plan to use that service. It's handy to have all the schedules available for planning.) Also note that the pass is not valid on the Nozomi Shinkansen, which are the fastest trains with the least stops. But the other services are still quite good; if you're making two or more long distance trips it's probably worthwhile. You can also use it for local JR service (including local services in Tokyo which serve as intra-city public transport) but that wouldn't solely cover the cost of the pass. But it can make a nice bonus.