An ongoing list. Aside from period dramas and films from the first half of the last century, Tokyo and thereabouts get the lion's share when it comes to film settings. So here's a list showcasing another, fast-disappearing side of Japan, with old tiled rooves, a temple or two, and, if you're lucky, some soft-spoken conversation.
These are all of the ones I could initially find. I'll add more as I come across them. Suggestions welcome.