Depending when you arrive, I'm sure there will be festivals going on at one point or another, so I suggest you should check those out. I know you're a guy Cevil, but I think you should give Shibuya a try, it's a huge shopping district in Tokyo (I've never been to Japan myself, but I've seen pictures, and Shibuya is like the Times Square of New York City!), if you want to see something pretty off the wall and unusual, then go to Harukuju, a place where many fans of visual kei will dress up almost exactly like their favorite band member, you'll also find gothic lolitas and other people who like to cosplay. These girls simply hang out and will let just about anybody take a picture of them, it's what they do for fun.
Try out their pizzas, I heard they replace the tomato sauce with octopus ink, and put odd toppings like potatoes and corn. Hmm, and tell me how the McDonalds there are like, hehe.
I think Japanese arcades would be fun, they have the best toys and gadgets that you probably won't see anywhere else. Such as this:
Dancing robots by SonyOh yeah, apparently the 7-11s there are like the perfect representation of what a corner store SHOULD be. High quality service AND food, lol.
And lastly, I think you should check out the different kind of candies they have, because Japanese candies are pretty unique ^_^