Basic Manners for Life in Japan:
A Common Sense Approach
Shoes
This is a simple one. Shoes are worn outside. Shoes are exchanged for slippers inside Japanese homes, small clinics or businesses. This fact will become so automatic that you will return home and immediately take your shoes off before stepping into your house. All your relatives will look at you funny.
If a building you enter has an elevated floor right after the entryway, and you see slippers set out and places for you to put shoes, this means you should take yours off before going any farther. When in doubt, lurk around until somebody else come in, then follow his example.
Slippers are hard to keep on, especially if you have big feet. Keep them on your feet by affecting a shuffling walk. If you lose one, step back into it and pretend nothing happened.
Don't wear slippers on tatami--it frays the mats. Step out of the slippers outside the door to the tatami room.
When going into the toilet area, exchange your slippers with the toilet slippers inside the bathroom. This keeps any messy stuff you encounter in there from being tracked all over the rest of the building. Remember to exchange the toilet slippers for your regular slippers when you leave, and spare yourself the embarrassment of returning to your party with a pair of brightly colored plastic slippers that have pictures of peeing cherubs on them.
Toilets
If it's a Japanese-style toilet (in other words, a hole in the floor), face the hooded area when you squat.
If you must step over the hole, keep hold of your shoes or slippers. There's nothing nastier than having one fall into the toilet--especially if you haven't flushed.
When using public facilities, bring a small packet of tissues with you. Toilet paper is a luxury, not an entitlement. Likewise, bring a clean handkerchief to use for drying your hands at the washbasin--paper towels are seldom available either.
Modern Japanese home toilets always use a handle for flushing. Therefore, when faced with an ultra-modern heated seat with a control panel that looks like it belongs on an F-16, look for the handle on the tank first. If you can't read the labels, don't press anything, or you may be in for a wet surprise.
Public Behavior
When shoved, don't get angry. Just stand firm or shove back. It's even better if you're wearing a shirankao (an "I don't know anything about it" face). Likewise, don't get too put-out if people don't hold doors open for you--the sheer volume of people in crowded cities like Tokyo would leave some poor, polite individual standing there holding the door until the building closed for the night.
While you'll see it occasionally in tourist spots, strolling and eating at the same time is considered rude.
Blowing your nose should always be done discreetly, in private. Always use a tissue. Nothing grosses bystanders out more than seeing someone honk the contents of his nose into a handkerchief and then stuff the snot rag into a pocket. Handkerchiefs are used to wipe the perspiration from your face in the summer, or to dry your hands at the washbasin.
Kissing in public is gauche. Save the lip-lock for when the two of you are alone.
Basically, don't do anything in public that will draw unnecessary attention to yourself. You'll get enough attention just by being a foreigner. :-)
Eating
When in doubt, swallow your pride and ask for a fork.
If you can use chopsticks, expect people to comment on it, even though you may have been eating takeout Chinese food with chopsticks since you were six. If someone start aggravating you too much with their chopstick comments, "accidentally" drop your food in the offender's lap (just kidding).
Don't stab things with your chopsticks or wave them around. Don't use chopsticks to grab dishes and pull them toward you. Use chopsticks to pick up food, and transport that food from your dish to your mouth.
When you're not using them, lay your chopsticks down flat against the edge of a bowl or plate, or on a chopstick rest if one's provided. Don't ever stick your chopsticks straight up out of a bowl of food.
If you're eating Japanese-style, with lots of small bowls, you can hold them up while you eat. It makes the passage from the bowl to your mouth much shorter and less disaster-ridden.
Don't get upset if people around you make a lot of noise while eating. While it's expected for diners to slurp noodles loudly (I think it cools them off before they scald your tongue), Japanese men have turned noisy eating into an art form. Apparently this is normal.