Visiting Places from Fate/Stay Night
Kōbe
Kobe Bridge
Kobe Port Island Kita Park
The foreground is almost the same if you shoot towards the bridge, but the lights shine in the other direction.

Weathercock House
Uroko House
Fudo-zaka Street
Kitano Street
There is a church on the left side of the street on top of the hill, but it is not the same church as in the visual novel.
The one on in the visual novel is based on Oura Church in Nagasaki. It’s actually said to be the oldest Christian church in Japan.
Akashi
Oda Family Nagaya-mon Gate
Hyogo Prefectural Archery Dojo
Chiba
Emiya Residence (Shōraitai)
The view of the Emiya residence backyard is based on Shōraitei, a tea house located inside of the Japanese Garden Mihama-en in Chiba.
Sadly the weather was not very good while I was in Chiba so the photos are a bit dark.