A good example - Amulet of the Lost Voices. An amulet related to a scribe of the dead which allows you to communicate with the fallen is found in a chest inside the temple of Jergal. It is a perfect fit for this location.
+1 but I can also imagine some cases where the loot might be a bit more varied, for example a dragon's hoard, bandit den, or the gobbo treasure room in the Shattered Sanctum - in those cases they could add loot that doesn't match the area theme but still makes logical sense.
