A lot of people ask me about Japanese customs. They learn the formal way to hand business cards, they bow deeply when they meet Japanese and they call me "Ito-san." Stop that. It's silly. To some Japanese, the awkward foreigners trying to please their hosts by acting Japanese may look cute, but more likely than not, you'll get a A for effort but you'll be forever the silly foreigner in their minds. It's only the extremely intolerant xenophobe who would really want a foreigner to really act Japanese and you don't want to be hanging out with those anyway. Keep an eye out for indicators of discomfort but bring the flair of your own culture with you.
Rather than trying to act Japanese, I suggest that people visiting Japan be sensitive and aware of the nuances in the interactions. It is more about timing, loudness, space and smiles than it is about how your hold your business card or calling people "Ito-san." When in doubt, shut up and listen. When smiled at, smile back. If you're freaking someone out, back off instead of continuing your interrogation. All of which I believe is not unique to being a foreigner in Japan. The more important Japan specific social behaviors involve cleanliness like taking off your shoes in homes and washing your body before and not taking your towel when entering the bath and not being stinky.
Caveat: If you're meeting someone for the first time, in a very formal setting, and you only have one shot, doing the step-by-step from the "How to Impress Japanese" book is probably a good idea. My comments above apply mostly to normal social situations.
UPDATE: I think many people were offended by this post. ;-) Please read the comments for an interesting discussion.