A map of where anime and manga are set rather than filmed, because nothing is filmed in a drawn show. 568 titles, 589 real places, 39 countries.
It has Washinomiya Shrine for Lucky Star and Hida-Furukawa Station for Your Name. It has nothing at all for Attack on Titan or One Piece, Slam Dunk is only Hiroshima, and about half the map is still just a city rather than the actual spot. (Working on it)
I have not gotten to the rest yet. If you know an exact spot, tell me and I might be able add it.
Free, no ads, no signup. Data is CC0.
It could use maps for Japan and for Tokyo specifically, because the map for Japan is pretty much a unified blob from Tokyo to Hiroshima.
Sorry, I will try to add a photo of only Japan for this post as well.