We checked out the entertainment districts of Chiyoda and Koto in Tokyo. On every corner their is some sort of anime figure shop (Although you may want to avoid these, there are also many Chinese knockoffs). We checked out some of thee largest arcades as there is a huge thriving arcade seen in Japan. Adults after a day of work can often be seen in their suits and shoes playing things like DDR or Super Street Fighter!
Claw machines and Gachapon (toy for coin gambling machines) also may a huge part of the Japanese ecosystem. Surprisingly enough, you should definately try the claw machines, unlike american ones, your chances to win are realistic! Themed Cafes should also be something that you take a look into. Popular animes and Mangas often have themed pop up shops that have a variety of dishes from or based on the concept of the stories. I, as a big fan of the Gundam fanchises, had to check out the Gundam cafe.