1. AkihabaraAkihabara is the world's most otaku neighborhood. If you're building a robot and need parts Akihabara is your best bet. It's also full of maid cafes, anime and manga shops, electronics shops and hobby shops (e.g. model trains).
2. IkebukuroIkebukuro is a massive shopping, dining and entertainment neighborhood in downtown Tokyo. It's well known for anime and manga shops that primarily target female customers.
3. NakanoNakano is the most densely populated residential neighborhood in Tokyo. It has a nerdy reputation. Nakano Broadway (near Nakano station) is an otaku oriented shopping mall. Its best known for rare otaku stuff and Dojinshi (self published manga). If you're looking for a life sized Ultraman model this is the place to go.
4. HarajukuHarajuku is a popular neighborhood amongst fashion subculture fans. It's often misunderstood that such people are cosplayers. In fact they're wearing Japanese street fashions — not costumes. The area is somewhat popular with cosplayers too.
5. NerimaNerima is a suburban district of Tokyo that was home to Japan's first animation studio. Today the area is still home to legions of animation studios including Toei Animation.
Nerima is also the fictional home of everyone's favorite gadget cat from the future: Doraemon.