Just finished reading Jeffrey Overstreet's Through a Screen Darkly, and thinking on his point that often it's one moment in a movie that gets through to your spirit, often in a way the moviemakers may not have considered.
Two that spring to mind come from successful mainstream movies, but the moments only marginally affect the movies themselves. The two movies are Crimson Tide and Waking Ned Devine, both entertaining, and both movies I've watched more than once.
But the moment in Crimson Tide that spoke most deeply to me was when the submarine was being prepared, in a downpour, to be sent out on its mission. On the soundtrack a wonderful male choir sang the hymn: For those in peril on the sea, with harmonies that came straight out of heaven.
In the other movie, it was music again that struck my soul. As the camera flew over the coastline, an Irish bagpipe was playing. The aching longing in that instrument had nothing to do with the comedy itself; it was something that belonged in the movie, yet was apart from it.