First off, the locations are near the Musashiseki station in Tokyo.
Now, you tell me what other anime used the same locations. The corner where the torii gates?
Go to this website to get oriented:
http://www.rinku.zaq.ne.jp/p_v/kojika.html
This website has the backgrounds from KnJ and the real world location.
I've found the torii gate corner, the corner where they turn around (two pics down), the playground, the Hey You! store, the railroad crossing, and the house that Rin and her mother is walking in front of, when they picked up Reiji at the "Futatsubashi" station. (Episode 6- Omoide) I found that one my mistake, I was wandering around in Street View, and realized the house I was in front of was the same one.