One of the things that always amazes me about Japan is how polite people are here. Yes some manerisims are different, if you are a Westerner, but the general respect and hospitality you'll experience in Japan is remarkable.If you are interested in making a good impression in Japan here are some things you can do:
Practice Japanese; even if you are not fluent, you might be superised how much your effort is appreciated.
Follow the rules! As a foreign person you may not exactly be expected to an expert on cultural courtesies, but please make an effort. If you are on a train try to remain quite, if you enter an area where shoes are not allowed take them off, don't stab chopsticks upright into your food ect. When in doubt, I try to follow the example of those around me. If everyone is bowing instead of shaking hand, I'll do that too.
If you are told no. Even gently and idirectly be respectfull.
Have fun! Japan is a great place to make new friends and learn a new culture.
Happy travels !