Proper manners in Japan are a bit different than they are in the US. For example, it's perfectly ok to sniff loudly if your nose is stuffed up, slurp your soup (which you can drink right out of the bowl) and noodles, and put your elbows on the table. Also, you don't see many people opening doors or giving up their seats on trains for women and the elderly; it does happen, but you don't see it as much as you do in the US. Though there are some things, such as not spitting on the street, that are the same in both countries. But if you want to display proper manner in Japan, here's some things to get you started.
1. Always take off your shoes at the proper locations. When entering houses, apartments, many shrines, some museums and restaurants, and random other buildings there will be a place to take off your shoes (usually a raised area), which you often swap for a pair of slippers of some sort. Note that, before stepping on tatami (woven straw) mats, you're supposed to take the slippers off as well.
2. Don't leave your chopsticks sticking out of a bowl of rice. They do that in funeral services so it's considered back luck to do it at other times. Lay your chopsticks to the side or on the lip of the bowl instead.
3. Don't use the little hand towel you get at restaurants on anything other than your hands and don’t use it as a napkin either. It's only for cleaning your hands before eating.
4. Don't point, ever. If you absolutely have to use your hands to indicate something, do it with more of a wave.
5. Don't blow your nose in public. Even if you have a tissue or handkerchief, it is considered very rude. Sniffing, however, is fine.
6. Don't brag and accept praise only reluctantly (usually after denying it two or three times). In fact, to be fully proper you should tend to play down your accomplishments, company, and family, any gift you're giving, etc until you’re forced to reluctantly accept that they're not quite as bad as you're making them out to be. Basically, play down anything that makes you look good and play up things that make the other person look good so you're praising each other, not yourselves). The one partial exception to this is things like job interviews.
7. If you know some Japanese, always use polite speech until you know enough to understand when it's ok to use informal speech (I’ll explain the difference in a future post). Even then, error on the side of caution.
8. If you get invited to someone's house, bring a gift (nicely wrapped if at all possible). Food or flowers are generally the most appropriate gifts. If you receive such a gift, don't open it right away unless the giver asks you to. Open it later when the giver isn’t around instead. Or, at very least, ask permission before opening it. The reason for this is so that, if you don’t like the gift, the giver won’t see your disappointment.
9. At parties, don't fill your own glass, fill the glasses of those sitting next to you and they'll fill yours in turn.
10. Avoid public displays of affection. Holding hands is ok, but things like hugging and kissing in public are heavily frowned upon.
11. Don't say "no". Not that you can't refuse a request or answer a question in the negative, but Japanese people go to great pains to do so without ever actually saying no. Unsurprisingly, this can be very confusing for people with a limited grasp of the Japanese language.
Note that, as a foreigner, you can pretty much ignore numbers 6 and 11 unless you're really trying to sound and act Japanese. If you don't really know any Japanese you can safely screw up 7 without offending anyone but, as all the Japanese words and phrases you're likely to find in a travel book and beginning Japanese classes are in polite form, it shouldn't come up. As for the rest of these points, you'll usually be forgiven (or at least overlooked) if you make mistakes here and there so long as you're doing so accidentally and not purposely ignoring them. The only one you really have to watch out for is 1, as wearing shoes wear you’re not supposed to (especially on tatami mats) is a major taboo.