Well, there are quite a few things...
Although I lived in Japan for 10 years, I am sure there are cultural things I still have no knowledge of, but I'll offer a few tips.
Bow to Japanese people when you meet them. This is especially true if it's a formal situation, or if they are older Japanese people.
Avoid too much eye contact. In other words, don't stare them in the eye.
Be very polite. American culture and others tend to be much more outgoing and informal, while Japanese culture is much more formal and honor based.
Learn how to use chopsticks properly, or just don't use them at all. Don't stick them in your food.
Don't make a lot of noise, don't try talking to Japanese people in a language other than Japanese unless you know they know it. Consider learning a few phrases like hello, thank you, how much? and where is the bathroom.
Well, that turned into a few more than I expected. Hope it helps! Also, it's better to ask a Japanese person a silly question than do something offensive.