Space Odyssey 2001. The Monolith is accompanied by a creepy male choir through most of the movie and is standing vertical. When the astronaut has his psychedelic journey he is staring at the Monolith as it slowly turns horizontal... The Monolith is the same dimensions as the theater screen. The only other time we hear the creepy male chorus is during the intermission when we are staring at a black screen. We are staring at a Horizontal Monolith.

In Jurassic Park, Hammond keeps saying, "I spared no expense." Ironically, when his programmer, Newman Dennis Nedry, runs into financial trouble, he refuses to give Newman Nedry a raise. So the disgruntled employee tries stealing dinosaur embryos and sets the disaster into motion.

In the Dark Knight, Joker is portrayed to the audience the way that Batman is portrayed to criminals. What do we ever find out about the Joker? Nearly nothing. He is a man with seemingly endless resources that arrived in Gotham, looked at the state of the city, decided that something must be done to change it, and so he offers his services to the criminals of the city. Not because he wants anything in return, but simply to "send a message". We never know what his real name is, where he got those scars, where he goes or what he does when he's not wearing the makeup. This is almost exactly what Batman is to the underworld. A man who arrived out of nowhere with all these gadgets and vehicles, who decided that he could change the way that Gotham was by doing the work that the police wouldn't do, and thus "sending a message". And in the same way that the police turn on Batman, and have to condemn his actions, the criminals of Gotham eventually sell out the Joker. The two are presented as two sides of the same coin. This is hammered home by the fact that two face is in the movie, a character who uses the same coin to make decisions about good and evil.

In Ferris Bueller's Day Off, FB's constant complaint, and his justification for many of his shenanigans, is that his parents won't buy him a car. Toward the end of the movie, when FB's mom is driving his sister home from picking her up at the police station, there's a quick throwaway line where mom complains that all this mess screwed up the deal she was working on, and that the money from that deal was going to be used to buy a Ferris a car. Ferris Bueller screwed Ferris Bueller.

Fight Club - Most people thought fight club was an anarchist/terrorist organization developed to take down the institutions that controlled society. However, the point missed was as fight club grew and as franchises got established it became institutionalized itself - and not unlike the institutions it sought to take down.

Jumanji. I didn't realize this until years later, but the hunter from the game board is the same actor who plays his father. Mind blown.

In Back to the Future, we see Biff spiking the punch at the dance. The same exact punch that we see Marty's dad drinking just before he decks Biff in the face. So George Mcfly got the courage from booze.

In T2, Sarah Connor attempted to kill an innocent Miles Dyson based on actions he had not yet committed. This was much like what the original Terminator tried to achieve by killing Connor for the child she had not yet birthed. In effect, Sarah had become the monster she was trying to escape in the first film.

Inglorious Basterds - it's not a hidden plot point so much as the overall allegory. The plot follows the propaganda machine led by Joseph Goebbels showing how movies were used to promote stereotypes of Jews and glorify the Nazi cause, when the other plot in the film is literally glorifying the brutal killing of Nazis. Tarantino gets the audience to cheer on the savage acts of the Basterds, and by doing so proves how easily it is to manipulate the emotions of the people. It's a really interesting way to show people how it's understandable that nearly an entire nation can get essentially brainwashed into supporting a tyrannical war mongering dictator.

The sword Will Turner made in the beginning of the first Pirates of the Caribbean movie. He made it for the Commodore (I forget his earlier rank), who loses it for a while, but regains it as Lord Beckett gives it back when he is reinstated. The Commodore is then killed by Davy Jones, who comments on the sword ("Hmm. Nice sword") after he stabbed him with it. At the end of the third movie, Will is stabbed by Davy Jones with the sword he made in the beginning.

Not exactly a plot point, but kinda funny. In Men in Black when they go to Edgar's house to talk to his wife, Will Smith's character asks for lemonade but spits it out back into the cup... It's because she wasted all of her sugar on Edgar's sugar water.