During the Iron Man/War Machine fight at the party, watch Pepper and Natalie. When the armored suits crash through the floor, Pepper screams and flinches, Natalie drops into a combat stance.
Another example at around 1:13:55. Take a look at the image on the right page of the book Tony is thumbing through. A three dimensional square within a three dimensional square. Otherwise known as a Tesseract. Seems the Arc Reactor may be based off research on the Cosmic Cube
In Film/Thor, a brief shot of The Infinity Gauntlet is seen in the Vault as two Frost Giants run by it.
The "FBI warning" on the DVD release has been re-written by Tyler as well.
Memento has one that puts a whole new spin on some of the plot. In a flashback scene in which Lenny is narrating the story of Sammy Jankis, a shot of Sammy sitting in a nursing home briefly changes to Lenny in the same spot and same clothes.
There's a similar effect in an earlier part of the story. Where Sammy is giving the finger after being shocked, one shot is of a longer and thinner hand than Sammy's is. Leonard's hands are roughly the longer and thinner shape.
Batman Begins. The "police officer" who recovered the Joker card was named J. Kerr.
Pirates of the Caribbean: At World's End: Pirate Lord, Diego De Leon, in the "Hoist The Colours" scene, appears to have a flag very reminiscent of Blackbeard's real-life flag. (However, in On Stranger Tides Blackbeard's flag is different.)
In The 6th Day, Sarah Winter's bare breast is visible for one or two frames as she sits up as the newest clone of Talia Elsworth
The theatrical cut (not the DVD cut) of Apocalypto has exactly one frame showing Waldo of Where's Waldo?, lying among the corpses of the mass grave that Jaguar Paw falls into. In the movie trailer of the same movie, one frame shows Mel Gibson himself, along with some Maya guys covered on white powder.
If you watch the commentary tracks of the Star Wars movies, several of these are explicitly pointed out. For example, in Episode II, during the speeder chase through Coruscant, there are briefly an X-Wing and a TIE fighter in the background, with the X-Wing chasing the TIE fighter.
In episode 3, there's a quick clip of a large number of moving ships with the Millennium Falcon hidden within the crowd.
In Return of the Jedi, when Vader is being electrocuted by the Emperor as he's lifting him in the air, freeze framing allows you to notice that you can see his skeleton and the various mechanical components inside.
ILM also did the effects work for Star Trek, and just like in First Contact, they snuck in a split-second shot of R2-D2 zipping past the Enterprise as it ploughs through a debris feild.
The 1988 feature-length version of Mike Jittlov's The Wizard of Speed and Time is rife with these; practically every effects shot has something hidden in it (such as sparks or lighting spelling out words one letter at a time). And the "speed" segment of the film-within-a-film of the same title has what amounts to Jittlov's manifesto on the power of the creative spirit written one sentence at a time into dozens of frames that go by in seconds.
In The Core, when pigeons have lost their sense of navigation and are flying into plate-glass windows, one of the windows finally breaks. If you freeze-frame on this moment, you'll see that the window is broken not by a flying pigeon, but by a flying trout.
The director actually makes it a point to specifically mention this during the commentary track, and to explain the circumstances behind it. While the animators were running tests to make sure all of the birds behaved correctly, one or more birds would often be temporarily replaced by trout models instead to make it easier to see those particular birds' paths through the swarming flock. Unfortunately, when they actually did the full rendering of the scene, someone forgot to change one of the trouts back into a bird, and no one noticed until it was too late to re-do the shot.
In X2: X-Men United, William Stryker's computer desktop is a treasure trove of shout outs. You'll see folders marked things like 'Victor Creed', 'Omega Red', 'Maximoff (2)', 'Project: Wideawake', 'Franklin Richards', and so many more!
When Xavier connects to Cerebro in X-Men: First Class, some familiar mutants from the comics can be seen if you pause, with a young Storm being the most notable.
In one scene of Tim Burton's Sleepy Hollow a demonic face can be seen in the fireplace; the makers point this out in the behind-the-scenes feature.
In the Serial Killer thriller Mr. Brooks, Dane Cook's character's first name is only revealed if you pause the DVD and look closely at the newspaper article about him in one of the last scenes of the film.
In Scott Pilgrim vs. The World, taking Scott's thought wheel frame-by-frame reveals some pretty funny responses/actions. The full list of responses and actions: "I gotta pee", "Who, her?", "It was nothing", "Pass out", "No, you are", "Tell Pac-Man story", "Uh...", "When's dinner?", "No speaka English", "Idiot!" "She's forty!", "She's nobody"
There's a brief scene in Attack the Block, where a map of the local area is shown. All the tower blocks and local streets are named after science fiction writers.
In The Avengers you can briefly see the shawarma place that Tony Stark recommends to the other Avengers after the final battle and the same one they're all eating at during The Stinger in the background after he crash lands when attempting to kill one of the alien dragons.
In The Book of Eli there is a hint as to what might have caused the end of the world on the map in Carnegie's office. If you pay attention you can just make out the outline of North Korea encompassing a THIRD OF CHINA.
In The Silence of the Lambs when Clarice enters the guard's station the camera pans around the room and passes over a bank of security monitors. One of the monitors shows Lecter's cell and shows Lecter getting up from his cot to get himself in position for his famous introduction to Clarice (and the audience).
When the Joker's semi driver is killed during the chase and Joker takes over for him you can see that the bullet holes in the windshield form a smiley face.
Right as Harvey Dent's face catches on fire the flames form the Batman symbol.
When Sal Maroni walks with his bodyguards to his car, right before he gets inside the car you can briefly see Two-Face grab his bodyguard and drag him away, which is how he was able to get inside without him noticing.
In Punch Drunk Love when Barry punches the wall in frustration the cuts on his knuckles form the word "love".
If you are paying attention to the flashback scene where Clark is pushed, there's a sign for "Sullivan's auto parts"
When Zod and Superman are fighting in a construction site, one of them is thrown into a sign with the common "Days since last accident" label. On the impact, the numbers fall, leaving a zero for a split second.
In Now You See Me, when the Horsemen first meet in the NYC apartment and see the holographic schematics, the name TRESSLER briefly appears.
In Twilight Zone: The Movie during the segment "Terror At 20,000 Feet" when John Lithgow's character opens the window and comes face to face with the gremlin, as he screams in terror a split second shot shows his eyes bugging out of his head and the veins in his head are visible.
In Jurassic Park when the Tyrannosaurus breaks through the top of the jeep to try and get at Tim and Lex, when it takes a bite out of the glass you can briefly see one of the Tyrannousaurus' teeth break, Joseph Mazzello who played Tim points this out in an interview.
At the very beginning of Anaconda when it shows the point of view of the anaconda as it swims through the jungle you can briefly spot a demolished boat and a dead man lying in the wreckage, presumably the partner of the poacher attacked shortly afterward.
In Jaws: The Revenge in the theatrical version in which the shark explodes after being impaled, if you pause the frames before the shark's head explodes you can see that the shark is just a toy model and is much smaller than the regular mechanical shark.
In Part III, as Doc and Marty discuss their plan at the train station, you'll see the clock for the (then-)new courthouse has the time at 10:04, which is when it will stop in 1955. Also, you'll see that the audience is actually introduced to Clara earlier, as we see her in the same background shot, waiting for Doc, who'd originally agreed to pick her up from the station. Since he apparently hadn't shown up, she takes the buckboard carriage which almost goes into the ravine before being rescued by Doc.
"The following peeview has been assproved for immature audiences only. If you can read this you are too close. Pee pee poopy boogers farts butthole. Rate I for Immature. We thought it would be funny to put this here. Kiss our asses and take it off pause."