-Have a walk in Ginza and have your camera handy.
-I highly recommend stopping at the New York Bar at the Park Hyatt for a drink in the evening. It's not cheap, but the view is just amazing and the jazz music is great. Its the bar featured in the Bill Murray movie Lost in Translation. Dress nice (pants and shirt) or they won't let you in... although they do offer free lender pants they aren't always the best fit. (which I had to use because I stopped by in shorts... yeah I know... but having pants that are 10 inches short from normal is always a good laugh).
-Shopping in Shibuya can be fun too if the clothing fits
-The fish market was awesome, but I'm not sure if it's still opened for the public.
-Tokyo Disney, nuff said.
-Super Autobacs store... wish we had them here (isn't there one in LA?)
-Akihabara is okay if you love computers/games.
-Have a beer in public
it's legal... just get one from a vending machine. Kirin, Asahi, Saporo, Orion...mmmmmmMmm
-If you have the time, head to Daikoku Futo in Yokohama port. Search for this on the interweb and you'll know why.
I could go on and on... had my honeymoon in Japan for three weeks last summer. Wish I'd go back soon!!!
Have fun!!