Some etiquette tips for Japan might be what you expect, but there are probably some things that you are not used to.
Waiting in line
It is common practice to line up not only to buy tickets but also when waiting for a bus or train. Often, you can find lines on the ground indicating where to line up for the next train. On the Tokyo Subway, for example, you can see where the doors will open and can line up there. The yellow lines at the edge of station platforms are there to keep people safe. Please stay inside the lines, away from the platform edge.
Regular trains, subways, and local buses in Tokyo are set up to transport the maximum amount of people. Aside from overhead luggage racks, there is no designated space for big luggage items (although you are allowed to bring luggage on the train). Good manners on trains is to keep your bags or backpacks close to you. When moving from the airport to a hotel or from one hotel to another, consider sending your big luggage items using a "takuhaibin" delivery service. Within the Tokyo area, delivery is usually within the next day.
Trains, subways, and buses in Tokyo have priority seats reserved near the door for the elderly, people with disabilities, pregnant women, or people with small children.
Some trains have “women only” cars, often marked by pink signs. Depending on which line you take, these cars might be “women only” during specific times of the days when it gets especially crowded.
Usually, it is relatively quiet on trains in Tokyo, even when it gets crowded. People usually keep their voices low, do not speak on the phone, and switch their phones to silent mode. If you want to listen to something, please use headphones.
Eating and drinking
It is common to eat on the long-distance Shinkansen trains, but not on regular trains and buses.
Smoking is only called at designated smoking areas at the stations.
Tickets and IC cards
Use a rechargeable IC card like the Suica or Pasmo card in Tokyo. It will make moving around smoother and you will not have to buy tickets at each station. Cards are available at train stations as well as Narita Airport and Haneda Airport. If there is not enough money to cover your fare left on your card, the ticket gate at the station where you get off will not open. Step aside and charge your card. Machines to charge cards are available inside the ticket gates as well as outside. Please note that Japan is still mostly cash only for charging IC cards and buying tickets.
Train etiquette is taken quite seriously in Japan, although you might see some locals who do not follow the rules. So on trains and around stations there are usually many posters that remind people how to behave with good manners on public transport. Some of these posters have quite a fun designs, so take a look.
If you are interested in learning more about Tokyo travel, click on these links.
Useful Japanese phrases for travelers - Here are some expressions and phrases to help you navigate Japan. If all things fail, a smile and a friendly attitude go a long way.
Japan travel tips for first-time travelers
Travel tips for eating and drinking in Japan - Including some basic phrases and Japanese manners
When you get sick in Japan and require medical care in Japan - Travel advice for when you are feeling ill
Travel tips: Visiting shrines and temples in Japan - What to do and what to expect, a short introduction