A lot of rules regarding indoor manners in Japan are related to footwear. A clear line is traditionally drawn between inside and outside, and outdoor shoes and indoor slippers are handled accordingly. These rules not only apply to most Japanese homes, but also to many traditional ryokan, some restaurants and the indoor sections of many temples, castles and other historic buildings.
For footwear purposes, the border between inside and outside is not the door itself, but the entrance area called genkan. The genkan is typically divided into a lower area where people take off and put their shoes and the elevated area that is usually covered by a different type of flooring and marks the beginning of the indoor living space. Don't step with your outdoor footware onto the elevated area. Likewise, when removing your shoes, try to avoid stepping onto the genkan's lower area in your socks. Lastly, it is considered good manner to turn your shoes to point towards the door after removing them.
When visiting a lot of historic buildings, it may be prudent for tourists to wear shoes that can be easily removed as you may be forced to put them off and on multiple times per day. Furthermore, make sure your socks are neat and free of any holes. During rainy weather, wet umbrellas and raincoats are supposed to be left outside or at the entrance or put into plastic bags to prevent them from dripping water indoors.
Slippers are provided by the host. If you are not wearing socks, it is polite to bring a fresh pair of socks to wear after removing your outdoor shoes because entering someone's house barefoot is not considered well mannered, although acceptable in informal situations. Slippers can generally be worn anywhere indoors except when entering rooms with tatami floor. Remove your slippers before stepping onto tatami and place them neatly outside the tatami room.
Furthermore, separate toilet slippers are often provided for use inside washrooms. The regular slippers are left outside the door when using the washroom. Don't forget to remove your toilet slippers after usage, a common faux pas among foreign travelers. See our toilet page for more details about how to use Japanese toilets.
Beyond the genkan, it is advisable to carry wheeled suitcases instead of pulling them - especially inside tatami rooms - in order to keep the floor clean and avoid damaging the sensitive tatami mats. Generally, be careful when placing or moving around luggage on tatami mats (and wooden floors) in order not to damage the floor. Some lodgings prefer luggage not to be placed onto tatami mats, altogether.
The policy on indoor photography at tourist spots differs from place to place. Most temples and shrines prohibit taking pictures inside worship halls. As for museums and historic buildings, the policy differs widely. Some allow photography, but others prohibit flash photography or any type of photography, altogether. Some tourist spots also prohibit the use of tripods, monopods and selfie sticks. Look for signs and ask the staff if in doubt.