I think that as a foreigner you are allowed to get away with a lot for a reasonable amount of time but if you are conscientious you will pick up what other people are doing.
But off the top of my head in no particular order:
1. Take your shoes off when entering a house you will get slippers. To be really polite turn your shoes to face the door after taking them off.
2. When you enter a house say OJAMASHIMASU! I think it means "I'm being intrusive!" - for the life of me I can't remember what you say when you leave! I think it is OJAMASHIMASHITA which means "I was intrusive" but I'm not sure....
3. Do not wear slippers onto the tatami floor of the house
4. Change house slippers for toilet slippers - Don't wear toilet slippers out of the toilet!!!
5. Wait to eat at the dinner table everyone will say ITADAKIMASU (let's eat!) together then you can begin. At the end of the meal say "Gochisosamadeshita" which means "That was delicious!"
6. If you are a guest your drink will be continuously topped up by the host if you serve yourself it's not too bad but then you must pour someone else a drink. This works at drinking parties also.
7. Try not to be too loud out in public.
8.Don't stand your chopsticks in food it is reminiscent of the death ceremony.
9. Wipe you hand with the moist towelette before eating and fold it nicely to the side of your setting.
10. Don't lick your chopsticks.
11. When complimented seem shy/embarrased and say "No it's not so!" or "You are being kind!" It's rude to be egotistical or brag.
12.When you see someone in the morning say "Ohayogozaimasu"
afternoon "Konnichiwa" and evening "Kombanwa" before you go to sleep say "Oyasuminasai!
13. When someone gives you a gift give profuse thanks, next time you see them say thank you again. This works for apologies also.
14. Business cards/name cards mark your "rank". Accept the other business person's card with both hands and a slight bow, look at it and make comments about the style or remark on the position at a seated meeting leave the card in front of you until the end of the meeting. When you hand over your card do so with both hands and a slight bow. They will do the same with your card.
Respect the other persons business card, don't pick your teeth with it, don't fold it and don't forget it.
15. If your chopsticks come in a paper sleeve when you are finished eating put them back in the sleeve and fold over the end then lay them on your plate.
That's just off the top of my head. For business there are many more complicated social mores to keep in mind. The way of entering an elevator, the seating arrangement in a car and the seating arrangement at a meeting are all very different from western perceptions.