Well, I haven't gone to Japan myself - but I did go to a short seminar once about preparing for a trip (mostly money saving aspects). This is what I picked up from it:

I guess there are these bed and breakfast type places that are a real money saver as far as living arangements. The guy I spoke with said they're much cheaper than a regular hotel, and a lot better in terms of an "authentic" Japanese cultural experience.

Another thing they mentioned is that it's a good idea to get a railroad pass if you're covering a lot of territory.

They also said not to tip waitresses, busboys, or housekeeping. I suppose it's considered an insult, because those professions are paid normal living wages, unlike in America, where tips are pretty much expected as part of your salary. I forgot to ask if it was okay to tip strippers.