・Do not enter a house with your shoes. This is one of the few rules for which Japanese will not make allowance just because you are a foreigner.
・Say "ojama shimasu" (sorry for disturbing) while entering someone's house.
・Do not stick your chopsticks vertically into a bowl of rice, as this is used in Buddhist funerary ceremony for a dead person.
・Do not pass food to someone else with your chopsticks for the same reason as above.
・Contrarily to Western manners, noodles can be and should be slurped. Likewise, bowls or plates should be brought up the the mouth rather than bending one's head toward it.
・Say "itadakimasu" once before eating or drinking, and "gochisousama deshita" to your host or to the restaurant's staff after eating or when leaving the place.
・Do not use your mobile phone in trains unless it is clearly allowed to do so. Using emails or SMS is fine.
・Japanese wash themselves before entering the bath, as they have a customs of sharing the bath water. This is true as well for public baths (sento) as for thermal spring (onsen) and bath in individual homes. The reason is that other people will use the same water after you.