See how we're doing in the Topsites Japan rankings. The Japan Railways network covers the entire country, over 21,000 km of line and 20,000 services daily. The company is divided into two main companies, JR East and JR West with lots of smaller regional companies. The minimum fare is 130 yen, which will usually do you for one or two stops.
All stations have automatic ticket vending machines.
They are quite easy to use as long as you're able to read the name of your destination in Japanese. If you regularly commute the same route, you might consider a monthly teiki-ken pass. Most stations have automatic ticket gates. JR services are generally frequent, regular and efficient. More and more trains have digital readouts in every carriage indicating the stops in both Japanese and English.