Ten Things to Remember in Japan

Shoes off at the entrance. Virtually everywhere you go 'the entrance' is lower than the house. The area just inside the door is called the genkan, and that's where you take your shoes off, step up into the house/inn itself, and put teh slippers on that are waiting for you. (Usually plastic, too small, and with no traction.)
When you get to your room, which is tatami, leave your slippers at the door and go in in your stocking feet.
When you use the toilet- which is usually communal in an inn- leave your slippers outside the door, put the toilet slippers on that are just inside the door, and repeat the process when leaving.
Note something about public washrooms in Japan- they don't have toilet paper. Department stores are the exception. Carry a bunch of those little packages of kleenex everyone hands out in front of the train stations. That's what it's for.
Note also that washrooms everywhere, practically, don't have paper towels. (Or hot water.) Carry a handkerchief for drying your hands. Do not carry a handkerchief for blowing your nose, because that disgusts people. Use tissues.
Japanese baths are usually communal in inns, but not usually mixed. If the inn has a rotenburo (outdoor bath- highly recommended) it often has a sign that can be put up saying 'In Use by Women' meaning everyone else stay away. Learn the kanji for 'man' and 'woman' so you know which bath to go to. The rotenburo are usually mixed, or at least mixable.
Bath etiquette: well, having undressed and stowed your clothes in a basket (usual for inns) or a locker (usual for bathhouses- sento), you take your bath stuff- washcloth, soap, shampoo, nailbrush, whatever- into the washing area. Some people let the washcloth modestly dangle over their genital areas in a gesture towards concealment, some don't. A matter of taste. You deposit everything in front of a tap, sit on the floor (preferably kneeling if you're a woman, but it's permissable to sit with your legs bent to the side. Or sit on one of the low stools provided. If you're alone, do whatever you please, but you're usually not alone.
Take a wash bowl, fill it with water, pour it over yourself. Try not to splash. It's inconsiderate of the people around you. Wash thoroughly, working up a nice lather. It's not the being clean so much as the being seen to be clean that's prized. Rinse it all off. Thoroughly. Rinse it again. The Japanese are watching in apprehension to see if you're going to go soapy into the bath, while you of course would never consider doing such a thing. If you have long hair, you're advised to pin it up for the bath, or to bind it back with one of those small handtowels that are useless for anything else. When you're washed and rinsed, you're allowed in the bath. Inns being places where everyone's on holiday and usually relaxed, I've always just gone into whatever bath/ pool is there. Sentos being an everyday place, it's sometimes a good idea to start by going into a bath where no-one else is. Then if they don't mind gaijin they'll come in too. And if they do they won't. You can get into a bath with people in it if you don't mind the possibility of everyone else getting out. Don't barge into the bath- sort of sidle in gently. This is a necessity because baths are hot as the hinges of hell usually and if you just step in you'll usually be very very sorry.
The basic rule for baths- wash first outside. No soap and no washcloths in the water itself.
At inns they give you yukata to wear (light kimono style robes made of cotton.) You can walk around the inn in your yukata. It counts as being dressed. In some hotspring places you can walk around the town in your yukata. The rule on yukata is that the left side goes over the right, opposite to what we think of as natural. The other way is how corpses are dressed, which is why you don't do it.
Meals are often served communally at inns, in the dining room. You go to the table where the name (usually) of you room is, though sometime s it's just sit where you like. To avoid scandalizing people, don't sit cross-legged if you're a woman.
The very polite way to eat is to take a little rice first, then a sip of soup, then whatever else you like. You're supposed to go back to the rice between other foods. A little fish, some rice, a little vegetable, some rice, a mouthful of salad, some rice. I don't see people sticking to this rule that much, but I mention it. Same with the 'pickles are eaten last' thing. The pickles are wonderful and in my experience get eaten all through the meal.
Don't stick your chopsticks upright in the ricebowl, supposing you're tempted to. It's how rice is offered to the dead. If it's a Japanese style meal, don't put soy sauce on the rice. It's vulgar, like dumping salt on a meal the cook has specially seasoned.
Be warned that a Japanese style breakfast is probably something you don't want. Grilled fish, miso soup, rice-- I know it sounds nice, but then you get to those raw quail eggs.....
If you're in a city, go to a coffeshop for a morning set, which gives you thick toast, butter, salad, and usually a cold boiled egg. (Sorry.) Plus coffee. The plus coffee is the draw, because you get a meal for what a cup alone often costs elsewhere. My breakfast of choice, I say without shame, was Macdonald's. Better than what they do here, especially the pancakes.
Note also that ko-hi- doesn't automatically mean hot coffee. You're advised to specify whether you want hotto or aisu. Aisu is served year round and is marvellous.
Don't look people straight in the eye, especially not in the countryside. You can do it in Osaka, but anywhere else it makes everyone hideously uncomfortable. Looking somewhere between the nose and the mouth most of the time and glancing at the eyes periodically works best.
If you're going to sit next to someone on a train, hesitate first, make a little bow, then sit down. That way you're not barging into their space. It's rude to walk in front of someone but often necessary, so do the hand thing- bend arm at the elbow and hold hand out in front of you, slightly tilted up, to indicate that you're passing through. Men sometimes jerk repeatedly from the elbow, which looks odd to me, but never mind.
Inns hang out the bedding for you, but if you stay in someone's house or in a place of your own, the futons are supposed to be aired regularly- daily is usual- hung out for a few hours then taken in before the afternoon heat or evening dew especially can get to them. The only season you can safely leave home with your futons hanging out is on sunny days in mid-winter. Any other season of the year, the sun is likely to turn to rain before a few hours have passed.
Generally: don't point at people; don't hand people money directly; say thank you and sorry a lot (the same word will do for both- sumimasen); be patient; don't stand too close unless you have no choice. (Japanese body space is actually larger than western body space, when left to its own devices.) Bring pictures of home. Bring a little present when you go to someone's house and give it to them as you enter. Never call anyone anata when you speak or try to speak Japanese. It's offensive most of the time except in certain circumstances, and you have to be Japanese to know what those circumstances are.