During the scene where the explorers are travelling to Atlantis via an ancient highway through several underwater caves in Atlantis: The Lost Empire, several masked warriors can be seen running away from their trucks as they approach. One of the warriors looks at the passing trucks before she runs off into the caves. This warrior is actually the film's heroine, Kida.
The bird from A Bug's Life. She is first seen attacking Flik and the circus bugs on the way back to the anthill, but she doesn't return again until the end of the film where she actually comes back to kill Hopper.
First is Boingo, the white rabbit who Flippers observes crossing through all four of the original suspects' stories:
Boingo first appears as a minor character when Red Puckett runs into him during her bike ride early in the morning. He confides to her having lost his job to the mysterious Goodie Bandit. A few scenes later, he is shown to be Red's cable car attendant, and is the only person on board when Red falls out.
Boingo happens to be the first passerby to show up after Kirk finds that his truck has been looted. This scene appears to be placed in between his two encounters with Red, given that he's holding the carrot crumpet she gave him during the bike scene.
Lastly, he shows up asking Granny for her autograph prior to the ski race.
When Flippers makes the reveal, all four of the characters' encounters with Boingo are shown Once More, with Clarity!: in Red's encounter, we see that Red fell not because of the doors malfunctioning, but because Boingo used his ear to depress a release lever. In Kirk's encounter, we see him lurking in the bushes as Kirk discovers the damage to his truck. In Granny's encounter, we see Boingo passing something off to one of the ski team members right before he asks her for her autograph.
In Red's story, when Red is coming to her senses after being pushed out of the cable car, Twitchy makes a three-second cameo as the squirrel who emits a camera flash from his mouth that blinds her for a second.
Near the beginning of The Incredibles, if you look very closely at the crowd attending Bob/Mr. Incredible and Helen/Elastigirl's wedding, you can actually see several superheroes such as Gazerbeam, Dynaguy, and Stratogale among the crowd. Those superheroes are later revealed by Edna Mode to have been killed by either the Omnidroid or by some cape-related accident.
In the first film, Pinkie Pie hinted at the existence of a human Alternate Self to Twilight Sparkle, which is confirmed in The Stinger of Rainbow Rocks, and fully debuts in third film, Friendship Games.
Oogie Boogie, the main villain of The Nightmare Before Christmas, actually first appears as a singing face on the Moon during the song "This is Halloween."
Doctor "The Shadow Man" Facilier, the villain of The Princess and the Frog, is first seen as a customer at the restaurant Tiana is working at as a waitress.
Even before then, Facilier can be seen a couple times in Down in New Orleans, the song that plays while Tiana is on her way to work.
In Shrek the Third, Shrek needs to find Arthur, and in his search, he has reached a football-alike field, to find out a brave, strong, handsome warrior riding a horse, attacking with a lance a poor excuse of a man. You have found the one and only King Arthur, showing off his supreme skills with a lance against a faceless, dull boy... oh, wait, it's the other way around. The handsome warrior is Lancelot, and the target is Arthur.
The Three Stooges has a little orphan named Teddy who gets adopted by a rich couple at the beginning. Turns out that Teddy later shows up when the Stooges are adults- and is at the center of the film's plot, without his knowledge!
When you're watching Toy Story 3 remember the cute little girl playing with a monkey who has cymbals, because she'll be coming back, as will the monkey with cymbals.
Wreck-It Ralph had a very interesting variation. In the beginning of the movie, M. Bison warns Ralph of "going turbo", making one think that it was a Shout-Out to his own games and how they had the "Turbo" title slapped on. When Q*bert warns Felix that Ralph ran into Hero's Duty, the Nicelanders panic, making it think that "going turbo" means "game hopping". When Felix and Calhoun end up in Sugar Rush, he tells her the tale of Turbo, a video game hero whose Attention Whore attitude caused him to invade another game and cause it and his game to be unplugged, thus making "going turbo" mean "going Turbo." Then, during the climatic race between Vanellope and King Candy, we learn the man's true identity....
Similarly, when Ralph gets his medal from Hero's Duty he gets attacked by a Cy-Bug and the two of them end up getting into a shuttle that takes them to Sugar Rush, where Ralph assumes the Cy-Bug died when it fell into a taffy swamp. Later, it turns out to be very much alive and also having made a huge colony of eggs, which later cause a Sugar Apocalypse.
In Yellow Submarine, Jeremy Hillary Boob Ph.D is introduced very conspicuously, complete with a character-introduction song. He then plays no role except light comic relief, and is kidnapped shortly after his introduction. In the end, he defeats the Blue Meanies once and for all, causing their leader to pull a Heel–Face Turn by... making flowers grow all over his body.
Duke Weaselton is apparently nothing but a common thief when Judy first encounters him, but turns out to be a supplier of the Night Howlers for the antagonists, whom Judy and Nick later have Mr. Big interrogate for information on who he was selling them to.
While chasing Weaselton, Judy saves the life of Fru-Fru, a young female shrew. She turns out to be the daughter of a prominent mob boss, placing the mobster in Judy's debt. This comes in handy more than once.