1). Take your shoes off
Shoes are never worn in someone's home or on Japanese traditional flooring (tatami mats). You may be expected to take your shoes off in a restaurant, hotel, hot spring resort etc.
You'll always be given a place to put your shoes. You'll also be given slippers to wear.
There are often different slippers for the bathroom. Never wear the normal slippers into the washroom (if washroom slippers are provided). Never wear the washroom slippers outside the washroom.
2.) Be quiet on your phone
Japanese people don't have loud public conversations on their mobile phones. People never speak on the phone in the train or in a shop. Most people keep their phone on manner mode (vibrate only).
When you go out for drinks it's rude to drink before cheers (Kampai!).
4.) Chopstick Manners
There are 10 basic rules of chopstick manners in Japan. The main points to remember are:
Don't use your chopsticks as a toy.
Never eat directly from common dishes — put it on your plate first.
Never stab something with chopsticks or stick your chopsticks in your rice.
Two people should never pick up the same food with chopsticks (i.e. if someone is struggling to pick something up you can't help them). This reminds people of a funeral ritual in Japan. It's downright morbid.
Avoid putting your chopsticks on the table. Use the chopstick holder.
Japan isn't an English speaking country. When you speak English, speak slowly and be patient. Learning a few basic words of Japanese is recommended. It puts you on the same level (as you struggle with Japanese the person helping you is struggling with English).
Tokyo escalators are strictly stand left pass right. As part of the Japanese tradition of having two opposite standards for everything , Osaka is stand right pass left.
Japanese onsen (hotspring) bath have fairly simple etiquette:
At most of the baths nudity is required. You can't wear a bathing suit.
Use the lockers. You can't bring anything but a small towel with you into the onsen area. Sometimes you need your own soap and shampoo (other times it is provided). Usually, hotels and ryokan provide soaps.
Use the provided showers to completely clean yourself before entering the bath. No soap can enter the onsen water.
If you have a tattoo you may not be allowed to enter an onsen. Don't get angry that's just the way it is (nothing personal). Everyone may feel uncomfortable if you have a tattoo. Generally, its not recommended to go to onsen if you have large tattoos.
Don't splash or play around in the water (it's not a swimming pool).
Be careful to enter the correct side of the onsen. Red is female, blue is male.
Keep your little towel out of the onsen water. Onsen pros put the towel on their head.
Never tip anyone in Japan. It's rude.
9.) Blowing your nose in public.
It's rude to blow your nose in public. Go to the washroom.
Acceptable loud noises are really different from country to country. There are many interesting noises you're permitted to make in Japan.
Bizengaust is a Russian-American lady who teaches English in Kyoto Japan and lies about her eye color on her drivers license since blue and green wasn't an option.