30 useful tips for travel in Japan

IC Cards and Smooth Transfer
Transportation
While in Japan, you will undoubtedly be using the trains quite often. Given the short time between trains, and transfers to different train companies, buying an individual ticket for each ride can get confusing, and also take a great deal of time if you are traveling with a group.
To solve this issue, most people use a plastic card with an "integrated circuit", called a "smart card", or as everyone calls them in Japan, an "IC card". You simply charge the card with cash at a train station, and can ride all trains by scanning it at the ticket gate. The card is scanned at your starting location, and scanned again at your destination, and the fare is then deducted. There are different cards from different train companies all over Japan, but they all perform the same function.

The first, and possibly the only cards you will get familiar with are the ones prevalent in Tokyo: SUICA, issued by JR, and PASMO, issued by Tokyo Metro. JR West, which is centralized around Kyoto and Osaka, uses an IC card called "ICOCA". A bit further to the east, in the JR Tokai operating area around Nagoya, a card called "TOICA" is used. Up until 2013, the trains all over Japan still operated on their respective IC cards for the region, but these cards have since been made universal, and it both advisable and convenient to stick to your original card.
Why it is advisable to stick to one card
Let's consider that you will obtain a SUICA card from a JR station (almost any station can issue them). You use the ticket machine to purchase a new SUICA card, and do the mandatory first-time charge of 1000-10000 yen. 500 yen of that will be kept by JR as a deposit. (The same goes for any IC card: there is a 500 yen deposit that will be kept by them as long as you have the card.) Do not bother with multiple IC cards from multiple companies, as you can simply use your one card in most areas in Japan.
Other uses for your card
There are indeed other uses for an IC card. Aside from only trains, major buses will have a place to scan your card, and nearly all conveniences stores accept payment by IC card. For small purchases, it is much easier to use a card, and even simpler than using a credit card. This system allows you to control your travel budget more, since you will be charging the card with cash, and avoid any possibility of not being able to use an overseas credit card. Also, remember that Japan uses many, many coins, and an IC card for small purchases will help you avoid having pocket full of change.