30 useful tips for travel in Japan

Do's and Don't's when Visiting Japan
As visitors to Japan, there are many customs and cultural differences overseas visitors need to keep in mind. There are some actions Japanese find very irksome, and although most will not physically stop you from doing something, we should all strive to be better travelers as tourism in Japan rises. As a general rule, be observant of the Japanese people around you, and if no one else is doing something, it's likely not a good idea. One does not need to adopt every single practice in Japan, such as bowing properly, but being adherent to rules and public order is what keeps Japan such a pleasant place to be. Here are some pointers on what are acceptable manners upon visiting Japanese establishments and homes.
On Removing your Shoes
When entering a private home, taking off shoes is not a suggestion, but an established practice. The issue is what to do when entering establishments and hotels. It varies from place to place. What you should look for is a step near the entrance. This would be for you to remove your shoes, and "step up" into the establishment. Many Japanese dining "izakaya" will have you remove your shoes first, or there may be an area to remove your shoes near your seating area before you "step up" to your seats. There will usually be multiple sets of slippers placed near the entryway or other area where shoes are to be removed. This is generally a good signal to take your shoes off.
You will use chopsticks at most Japanese style restaurants, unless the food is better eaten with a fork or spoon in which case, that is what the shop will provide. Chopsticks are not usually brought with the food, but usually placed in a receptacle at the table. Food is rarely eaten with your hands in Japan. Interestingly, though, sushi can be eaten with your hands. In fact, this is the traditional, and what many consider the proper way to eat sushi. Although you are confident with your chopstick ability, it is recommended to eat sushi with your hands. This is to eat the sushi quickly and in one bite when the chef serves you. For "kaiten" conveyor belt sushi places, take the entire plate off the conveyor belt with the sushi on it and place it at your table or counter seat. The tab is calculated based on your number of plates, so please keep all plates at your table.
Lining Up
Japan, and in particular Tokyo, is very crowded. Yet, you will find that things tend to move along quickly despite the huge amount of people. At the root of this is the practice of forming neat lines in all situations; for trains, for food, for buying tickets, at the register, literally everywhere. In stores or otherwise, always be conscious of where the line begins, and please do not cut under any circumstances.
Dealing with Garbage
You will soon notice Japan's lack of public garbage cans. This encourages people to be more mindful of their trash, and ideally dispose of it when you return to your residence. There are, however, recycling bins near vending machines for cans, glass, and plastic bottles. Feel free to use them, but please do not dispose of your other garbage items in them.