At the end, the Innisfree villagers pretend to be Protestants cheering the visiting Bishop in order to trick said Bishop into letting the Protestant Minister Playfair and his wife stay. Leads into the closing scenes of the major cast of villagers waving to the audience.
On a meta level, director John Ford's brother Francis (as the town elder) getting a solo "hurrah" shot at the camera. This was a personal project for John, and he wanted his older brother get a good part in it. Francis died less than a year later.
The romantic scene of Mary Kate and Sean (I know, JOHN WAYNE) kissing under the cover of a ruined arch during a rainstorm.