This one is important because chopsticks are used to eat almost everything in Japan.
First thing, never put your chopsticks upright into rice, because this is part of a ritual conducted at funerals when offering rice to the spirits of the deceased.
Also never pass food from chopstick to chopstick because again, this is done during funerals to pass the bones of cremated relatives. Obviously, this kind of imagery doesn't go down well over dinner.
Additionally, do not eat directly from common dishes with chopsticks; always take the food and put it on your plate first, and then eat it.
Don't point your chopsticks at people too, as this is considered very rude.
Lastly, never do rubbing of chopsticks. You know when you open some wooden chopsticks and do that rubbing to get rid of splinters, and just because it's fun. Just don't do it in Japan because it is considered rude to the owner of a restaurant, implying that you're basically saying, "Oh, your chopsticks are probably cheap." Let's face it, they probably are.