what are naturally generated structures that appear in the overworld

Answer 1

Villages, strongholds, desert temples, jungle temples, End portals, abandoned mineshafts, dungeons, witch huts, swamp houses, desert wells, ores, trees, and libraries (found in strongholds).

Answer 2

There is the jungle temple which spawns in jungle biomes, the desert temple which spawns in desert biomes, villages that spawn in plains and desert biomes, and wells that spawn in desert biomes. If you're playing a water map, there are villages that spawn underwater instead.