Hidden around in many unexpected places, you can find several interesting anime/manga connections in Suginami, Tokyo. Check here for information of cafes, bars, and even parks and other sightseeing.
Anime-Themed Bar in Koenji
Manga Cafe and Bar in Ogikubo
Small Park Designed by Hayao Miyazaki in Asagaya
Cafe with Anime/Manga Covered Walls in Ogikubo
A Museum Dedicated to Japanese Animation
Anime Bar in Asagaya