You haven’t seen Gremlins!!! Please rectify that.
The Dad is an inventor whose machines never work properly. He’s at an inventor’s convention. While phoning his wife, many inventions can be seen, including the Time Machine from the movie of the same name based on HG Wells’s book, and in one shot it’s there being operated, and in the next shot it has vanished.
Last Crusade had another bit where Indy says “Ah Venice” three times, the first when he originally gets to the city, the second where he and Dr. Schneider climb out of the catacombs into a crowd of people, and the final time when he spends the night with Schneider.
I am serious! And don’t call me Shirley!
In “A Million Ways To Die In The West”, Neil Patrick Harris accepts an invitation to a duel with Seth MacFarlane by saying “Challenge Accepted!” .
His character Barney Stinson always said the same thing in “How I Met Your Mother”.
In “The Lion King,” Simba tells his uncle “You’re weird, Uncle Scar.” To which Scar says, “You’ve no idea.”
Scar was voiced by Jeremy Irons, who said the exact same line as Claus von Bulow in “Reversal of Fortune” a few years earlier.
well, if you’re going that one, one UN-subtle joke was from the end of the Barbra Streisand- Ryan O’Neal comedy What’s Up, Doc?", where , at the end she says “Being in love means never having to say you’re sorry,” then blinks rapidly several times.
O’Neal’s character sits stunned for a few second (which gives the audience laughter time to die down), then responds “That’s the stupidest thing I’ve ever heard in my life.”
(And, if you don’t know, that was the famous line – and tag line – from O’Neal’s recent tragic tear-jerker Love Story.
(In a similar vein, I loved how Daniel Craig’s James Bond first responded to a bartender’s question about whether he wanted his martini stirred or shaken – “Do I look as if I care?”)
In Return of the Swamp Thing (yeah, yeah, I know!), Louis Jordan’s character has a parrot named Gigi.
Jordan had starred in the 1958 musical Gigi. I may have been the only person in the (very small) audience who got that joke.
“Waiting for Guffman” - the Chinese restaurant scene is opened with a shot of the giant neon-lit “Chop Suey” sign Waiting for Guffman- Chinese Restaurant Scene - YouTube - and the first words of dialogue inside are “How did you find this place?”
I’m not sure what movie this is from (maybe Wallstreet?).
A group of people are siting around a very modern, “stylish,” impractical coffee table, which has a top made with irregular holes in it.
One of the people puts his coffee down on the table, and it falls though one of the holes and crashes to the floor.
Most of the people who I’ve talked to about this scene think are puzzled by it - they think he was being a jerk, and did it deliberately, or was clumsy. But, it’s really just a gag about rich pretentious assholes and non-functional furniture.
In A Christmas Story, the Chinese restaurant is in a former bowling Alley. They kept the sign and made the name of the restaurant “Bo ling."
I’ve watched this movie at least 15 times every Christmas, and never noticed this.
My life has been a complete joke 
In the movie Bill and Ted’s Excellent Adventure George Carlin shows up in a phone booth, which is a reference to Doctor Who where the main character travels around in a British Police phone box.
People who have never heard of the movie crack up when they say any sentence with “surely” in it, and you respond “Don’t call me Shirley.”
In Police Academy, the hooker hiding in the lectern is played by Georgina Spelvin. Very famous porn actress, arguably one of the bigger names in the movie, but you would do remarkably well to figure it out.
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Wizard of Oz:
Scarecrow: [about the Flying Monkeys] They tore my legs off and they threw them over there. Then they took my chest out and they threw it over there.
Tin Man: Well, that’s you all over.
Actually it was Mozart.
I think another subtle joke is that the kids died.
On the topic of subtle jokes in Superman, there was another one in the second movie. When Superman had saved the kid from falling, if you listen closely you can hear a lady say “What a nice man. Of course he’s Jewish.”
And I just thought of some more. The Shrek movies have a lot of subtle jokes. In the first movie when the Magic Mirror is showing Fiona to Farquaad on repeat, if you watch closely you can see him get a boner.
In the potion factory in the second movie, one of the bottles is labeled Viagra.
In the fourth one when Shrek says “My donkey fell in your waffle hole” Fiona thinks he means… yeah.
In The Cask of Amontillado when Montresor says “Yes, for the love of God, Fortunato!”, Fortunato probably thinks he means he’s doing it for his love of God.
D’oh! Was it? I was thinking it was Beethoven because the same riff appeared in the Trans-Siberian Orchestra “Beethoven’s Last Night” soundtrack. Classical music isn’t my strong point… (clearly!)
In Iron Man 2, when Tony Stark asks Natalie Rushman if she actually speaks Latin, she says “Fallaces sunt rerum species. It means you can either drive yourself home or I can have you collected.” However, what the phrase really means is “The appearances of things are deceptive”.
Batman Returns: Bruce meets up with Selina, and apologizes over the hasty interruption to their previous date.
As Bruce and Selina start slow-dancing together, Selina lets out a little contented sigh.
Bruce: “So, no hard feelings, I hope?”
Selina: “Actually… semi-hard, I’d say.”
Errol Flynn in the 1943 movie “Northern Pursuit” at the end assures his fiancée that she is the only woman he has ever loved and turns to the camera saying “what am I saying?”, a reference to his recent acquittal in a rape trial.