Be aware of the little tray thingy they use for all exchange of money - when paying for something you put your money into the tray, and they will place any change into this tray for you to take. I got a few confused looks when trying to put cash into their hands, although I guess they must be used to foreigners doing this. It does make it a lot easier to dig out mounds of coins though, it's really easy to build up a big collection of them.
I completely forgot about the not eating while walking thing and did this often... I guess they're used to foreigners doing this in large cities too, I didn't notice any strange looks. Although if you know it's better to try and be polite!
There's some places you can't take photos... such as in pachinko parlours (although the guy was very nice and apologetic and bowed a lot as he did the 'dame' cross arms sign and asked me to put away my camera) and I think in parts of some temples.
If you ask someone in a shop for directions, be aware that they might leave what they're doing and escort you right to where you need to go. I always felt a bit bad about interrupting their work when all I wanted was for them to point in the right direction!
If you're just going for a holiday don't worry too much if you don't have a fantastic grasp of Japanese - in the larger cities and tourist areas they speak bits of English and you can get by alright with this and some miming. And there's no need to be embarrassed of less than perfect Japanese (like I was for the first couple of days of my holiday) - everyone is generally really encouraging, impressed and genuinely flattered that you bothered to learn even a few words of Japanese. I think it's also polite to be encouraging when Japanese people try to use English because they're overcoming their embarrassment and trying hard too
