Akihabara. Otaku central. I've been to this area several times before now and still, it really sets itself apart. It's best described as a mecca center for geeks. A large portion of the other stores in this area explicitly cater to people with obsessive interests. Video games, anime, manga (comics), robotics, toys, etc. It's all here.
Super Potato is known to be one of the largest and arguably greatest retro video game stores in Japan and possibly the world. It hosts three floors of nothing but classic video games, consoles, memorabilia, combined with a retro arcade on the top floor. Beyond just being an awesome place to shop, you take home an experience with you at the end of the day. As a part-time nerd, I will say this place is well worth the venture to find.
Famicom cartridge chair.
My size Gundam.
I accidentally found the Good Smile Cafe here. I believe this location opened between my last visit and now. Good Smile has been producing figures since 2001 and has become one of the most popular distributors in the business since.
Hatsune Miku leek cake thing.
Full scale Hatsune Miku.