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.
A downplayed example is at the end, when Sean finally gets Mary Kate's dowry money from Will, he moves to throw it in a furnace, and she rushes to open it for him without any hesitation. This proves that she didn't care about the money, and once he shows that he's willing to stand up for her, he has her unwavering loyalty.