The best basic tips I’ve seen for navigating Japan in a way not to offend is on this post at Conde Nast Traveller – The Essential Things to Know Before You Visit Tokyo.
The most important tips are:
- Greet people with “konnichiwa”. Add “san” (or “sensei” for a teacher) to the person’s name. Return bows.
- Wear decent clothes. Bear in mind that you’ll be taking your shoes off at every restaurant.
- Say “arigato” (thank you) in all interactions.
There is more information on the post, so go read it! The only thing that I would add to the information, is that most taxis over there have automatic doors. The driver will get irritated if you manually close their automatic car door in my experience!