There are a lot of specific etiquette rules you could go over, but you could do that forever and never cover them all. Plus people here have already mentioned the important ones. I lived and worked in Japan for several years; here are my thoughts to make things simpler for you:
1. People say "thank-you" a lot. It's "arigato" or "arigato gozaimasu" or "domo arigato gozaimasu" (longer being more polite). You'll hear it from everyone about all sorts of tiny things that wouldn't be acknowledged in most other countries. Just go with it. If you can learn to pronounce it with a decent accent, try it yourself. You can never say it too much, as a rule of thumb, or say it at the wrong time. It's normal to nod the head in a sort of mini-bow as you say this, a deeper bow being more polite.
2. Observe people around you and copy. If they all walk on the right side of the street, do the same. If they're speaking in hushed tones, do the same. If they take their shoes off before going in somewhere, do the same. If they don't take umbrellas inside with them, do the same. Nearly all etiquette can be covered if you are observant and just copy.
3. Quiet is good. Some foreigners were very noticeable when I was in Japan due to this. A group of tourists would get into a train full of silent people on their way home from work, and start talking as though they were in a bar, almost shouting. No-one would say anything to them, of course, but it would always stand out as rude and unobservant. Try not to be the loudest person in any place.
4. Japanese etiquette is based around a simple rule: make others feel good. So don't be too loud if they're being quiet and obviously want peace, say thankyou and show appreciation, don't stare at people (eye contact is similar to the west in Japan, although it varies a bit place-to-place so just copy what you see others doing), don't be raucous...
5. People aren't stupid. They'll know if you're trying to be polite even if the way you do it is different, and appreciate that. I took part in a survey to this effect once; they found that in Japan, people feel grateful if you try to be polite even if you accidentally end up being rude, whereas in western countries people mostly only feel grateful if your final actions are polite, no matter what your intent might have been. As long as you are trying then you're fine. No-one will really care if you put soy sauce on the wrong thing as long as you don't eat with your mouth open and spit food everywhere.
I presume you don't speak much Japanese, since a great deal of their etiquette is tied in intimately with the structure of the language. That's fine, but it helps if you learn a few words, even if only "thank you" and "yes". It can help to watch a Japanese film (with subtitles) showing a bit of everyday life, just to show you how people normally go about their day and to calm any nerves you have.
