There are lots of ideas littered throughout this forums on where to go and what to do, but, the one thing you should try to do is exchange your monetary funds with somebody who wants to sell their yen for your $$ or whatever you happen to use. This way, you can get the exchange rate of what it is on that day and bypass the bank or exchange fees that all monetary institutions will charge you with when you get to a facility that handles this. This will mean some legwork for you to do the research into who is willing to do this, but there are always people returning from Japan with extra yen they know not what to do with, and so their immediate response is to save it or go to the bank and exchange it...If you know of somebody (most likely from a Japanese company) that wants to do this, you both win.
Now your particulary nation may have certain laws regarding this, so you may want to find out what is legal or not, but, personally, a monetary exchange so that the banks don't rip you off should be ok (it's not like you are selling drugs or laundering money)
And get yourself a Japan Railways Pass so you can use the JR rails without having to pay over and over again (unless you plan on staying inside Tokyo only).
just my two yen's worth....