I have to cast a bit of a dissenting note here -- Japanese Customs can be a bit of pain in the rear, because they will generally stop everybody in the green lane who looks non-Japanese and ask a few questions, and if any alarm bells ring or they don't like your haircut, you'll get your bags searched and a lot more questions. All done quite politely, mind you, but I don't know of any other country (bar Israel) where this happens so regularly. I've generally found it useful to not speak any Japanese in these situations, it makes interrogating you too much a hassle for them...

And oh yes, if you are caught with something you shouldn't be caught with (ranging from OTC Sudafed to a kilo of Colombian pharmaceuticals), you might like to know that you can be held incommunicado for 21 days, during which the police will resort to anything and everything short of torture to make you confess. Don't sign anything until you've seen your embassy rep and had their recommended lawyer approve, otherwise you'll end up like this guy, or this guy, or this guy.