30 useful tips for travel in Japan

Highway and Regional Buses
Japan’s efficient and low cost long-distance and highway bus companies that ply the main highways and link major cities to regional towns and tourist destinations across the archipelago, can be a good way for overseas visitors to explore Japan. However, only a few highway bus companies offer information and web sites in other languages.
Highway Bus versus Train
However, if you can get around the language issue then bus travel can have many advantages over train travel, mainly because it is often half the cost or less, and they have the advantage of traveling long routes overnight, therefore saving time and accommodation costs. For example, the overnight highway bus from Tokyo to Osaka is about ¥6,000 or less versus ¥14,000 if you go by the Shinkansen bullet train. Also, in rural areas, bus lines have replaced some rail links or are faster than going by rail or air. For example, it is much faster to get to Tokushima in Shikoku from Osaka by bus than it is to go by train.
Highway Bus Accomodations
Moreover, long distance buses usually allow you to carry at least one large suitcase in the luggage compartment, unlike most trains that don’t have much luggage space. They usually provide a toilet, reclining seats, and are air-conditioned. The downside is that they are generally slower, often less frequent and a bit more cramped than trains. They will stop every 2 or 3 hours for a 10-15 minute break at a service area where you can buy drinks and food. Highway buses have seat belts, and although the buses are very safe with highly skilled drivers, it is requested you wear them.
Local Buses
In larger cities, you can get away with just relying on trains and walking to get to places, but you will find very quickly that as you leave city centers, a bus is the primary option in many cases. Buses in major metropolitan areas are "pay beforehand", meaning you pay a flat rate when you get on the bus, and can ride until the end. In this case, the buses usually have you enter from the front door, and insert money right away into a machine near the driver. There will also be a place to scan your IC card (SUICA, Pasmo, etc) to pay instead of using cash.
In more rural areas, however, the fare will be relative to how far you ride the bus. There will usually be a ticket dispenser once you step up onto the bus. Take one, and when getting off, place the ticket into a machine near the driver along with the correct fare. Many of these machines will not dispense change, so please confirm with the driver if you are unsure. These buses are generally entered from the middle door of the bus, and exited from the front door.
The best advice for riding a bus in a more rural area is to know exactly the stop you need to get off at. The bus stops are numerous, and many times will be displayed in Japanese only. It can be difficult to hear the announcement if you're unfamiliar with the name, even if you prick up your ears and listen very carefully. The best advice is to first voice your destination to the driver to confirm if the bus is the correct one. Then, when riding, sit or stand near the front, and almost certainly since you voiced your destination to the driver, they will signal that your stop is coming.