That whole "giri" (obligation - sort of; duty - sort of) thing, and culturally knowing what you can/can't do, should/shouldn't do. Ranges from which words to use in a conversation depending on the "status" of the person with whom you're speaking, through making sure you don't leave your hashi in the bowl and which sauce goes with which food, through everything else in general behaviour.
Actually, while I totally get what you mean, the more appropriate term for what you are talking bout is reigi (礼儀), which means etiquette or politeness. You essentially have to learn 3 ways of speaking to people in Japan - informal, the way you would talk to a friend, family member, inferior (kouhai!!!!!), someone younger than you, etc.; cordial, the way you would speak to a school teacher, someone else's parents, someone you don't know, etc.; and formal, the way you'd speak to your boss, martial arts teacher (though, after a while, you may be able to drop back to cordial), etc. It can get pretty hectic, especially because there is so much of a tendency for people to over use polite, formal speech by stacking honorific words on top of one another, that now, simply speaking correct formal Japanese is not enough in some situations. You have to speak nijuu keigo (二重敬語), double-stacked respectful speech.
The chopstick thing is actually kind of interesting. The way it was explained to me was that because in buddhism, when praying at a funeral, you light sticks of incense and stick them into a bowl of sand, sticking your chopsticks into your rice bowl makes an impolite suggestion about you praying after the death of the person across from you. It's not a straight line of logic on the insult side of things, but you get it. "I'm not dead, so don't act like it" sort of thing.