“The Betrayal” (S09E08) is a an episode-long reference to the film Betrayal (and the play that came before it). In this case, it’s only subtle because of the relative obscurity of the reference, though. There’s nothing subtle about an episode that runs backward.
Just thought of another one: Frank recalling his bad experience as an Army cook is an obvious reference to “Platoon,” but the scene right before that, when he pours himself some Scotch and settles back to tell his story, almost seems like a parody of something else. Maybe “Apocalypse Now?” Or just a general parody of similar scenes in various old war movies?
“It was War, Frank; it was a crazy time for everyone.”
If you click on the “Connections” link on an episode IMDb page, you might find some nice movie references others have caught.
E.g., for The Glasses S05E03, George does the same “spot a dime” bit that was used by Donald Pleasance in The Great Escape.
In The Bris S05E05, in addition to all the Godfather references, there’s also the Pig Man/hospital thing which references the Malcolm McDowell film O Lucky Man!
The scene where Newman is following Kramer in a mail truck and warning him to stop his vendetta against the US Postal Service is an homage to “Three Days of the Condor”