They are all different. Some have everything in one store. Some have different genres on different floors. Shinjuku has a main used store with all genres and several stores that focus on individual genres. All locations have used CD's. If you are in Shibuya, Recofan is worth a visit as well - it's near the Shibuya DU. I would use my CD buying time in Tokyo. What area of Shinjuku are you staying?