Toy Story 2 did this with the scene where Buzz is karate-chopping through the bush — look real closely at the last twig he chops: there is a tiny caterpillar crawling across it. This instance was later referenced in the bloopers with Flick and Heimlich appearing on it.
Also, when Hamm is flipping the channels looking for the Al's Toy Barn commercial, the images that flash by are from older Pixar shorts and commercials.
Not to mention the Disney Pixar Star Ball popping up everywhere...
Toy Story 3 had a moment where if you paid close attention it was possible to see that one of the two garbage men is Sid from the first movie.
In Atlantis: The Lost Empire, as the window of the submarine descends, an extra waving at the camera is visible for a few frames.
In Lilo & Stitch, Stitch hits Jumba with the VW Beetle and knocks him into Nani's bed, over which hangs a poster of surfing legend Duke Kahanamoku. When Stitch pins Jumba with the Beetle, Duke briefly has a shocked expression on his face, visible for only a fraction of a second.
Carpet is in the same shot as Belle in Hunchback. Carpet also pops up near the start of The Princess and the Frog, which has several other references by that point.
Pumbaa shows up in Hunchback too — as a roast pig on a spit.
During the production of The Rescuers, one of the animators decided to pull off a prank, and inserted an image from Playboy into a few of the frames. Normal viewing could not reveal anything, but a careful freeze frame did. When it was spotted by Disney, the image was edited, and all subsequent VHS and DVD editions were Playboy-free.
Similar to the Cinderella example below, Bernard's current cover pose for The Rescuers can be seen for a few frames during the "Tomorrow Is Another Day" montage to Devil's Bayou.
The Rope Bridge sequence in The Emperor's New Groove features a moment when some boards fall into the chasm; if you slow it down enough, you can see they are stylized letters spelling out "D-A-M-N".
In 9, if you pause before 8 walks in front of one of the statue bases, whilst outside the library, you'll be able to read the sign in the background: "Cheer bad and cheer good and shadows which we cast". Not sure whether it means anything, but it sounds cool.
When Cinderella gains her magic ballroom gown from the Fairy Godmother for the very first time, if you pause at the right moment when she is spinning in her said gown, for a split-second you can actually see her in the very pose they used as stock clip-art for her merchandise.
More verifiable is the train that destroys the Dipmobile at the end. Close examination reveals a murder is taking place in each compartment window.
During the car chase scene with Eddie and Roger trying to escape from the weasels, you can see that Eddie is replaced with a hand drawn cartoon in some scenes when the car spins around or goes soaring through the air.
In the first, there are several bonuses that count as foreshadowing examples, and might be overlooked until another character's story gets told.
If you look carefully during Red's mine cart ride with Japeth, when they pop out of the tunnel, you see the drop they go down with a POV shot. Another driverless cart can be seen scooting by on the track Red's cart goes under. You might make out two individuals on it. When you freeze it, you will notice the Wolf and Twitchy. In turn, when the Wolf gets to this point in the story, (just after he says "Now this is a shortcut!") they pass by another track that has a steep drop down the hillside that goes under their cart's track, and you hear a scream as a cart drops in the background. Freeze the image at the moment of the scream, and you can see Red dropping in her mine cart.
When Red is looking at the map of the mine tunnels in Japeth's shack during "Be Prepared," if you freeze it, you'll see places with such punny names like Puckett Grove, Sam Hill, Kanbar Kanyon, the Blue Yonder, Murphy's Low, Boulderdash, and something that looks like it says "Old Man's Cave" (partially obscured by Red's head).
When Red is in the treehouse and reading a travel magazine, if you freeze at the right time, you'll see that she's looking at a cartoon of what appears to be a rhino and zebra having tea.
When Red falls from the cable car, right before she slips, Boingo's grab is far more at her basket than her. Also, when Red is plummeting, you can see him looking down at her - but his expression is one of anger rather than one of concern.
Red's confrontation with the Wolf has her use Mace spray on him. If you freeze the image at the moment she pulls it out, either in her story or in the Wolf's story, it clearly says "Wolf Away Spray". Which leads to the revelation that Red is Crazy-Prepared.
Twitchy only makes a three second cameo in Red's story, during the bit where a flashbulb in his mouth goes off.
When Boingo is Storyboarding the Apocalypse to Red, you can see that his proposed "Boingoland" will extend into Smallville, and also has an airport, an amusement park, and a lot of other intersting things relating to him.
In the second, the recipe for the MacGuffin is briefly on screen. If you freeze the image, you can see amusing fantasy-story entries like Sleeping Beauty's morning coffee, but right at the bottom is Soylent Green, crossed out with "People!" written beside it.
In Kung Fu Panda, in the "you are free to eat" scene, if you pause just as Shifu snatches away the first dumpling Po tries to eat, you can see he's practically making a Troll Face.
In Kung Fu Panda 2, during the scene where the heroes are captured and Po puts Mantis inside a cage, you can scroll along frame-by-frame and see Po swapping out the real Mantis with his wooden action figure.
In An American Tail: Fievel Goes West near the end of "Dreams to Dream" as Cat R. Waul is carrying Tanya away, there is a crudely drawn penis and testicles next to Tanya's open mouth for one frame.
In Astérix Conquers America when a beggar pretending to be legless stands up and runs, his genitalia is exposed for a couple of frames.
In Oaken's shop, you can see a small plush Mickey Mouse on the lower shelf.
The Canadian animated short The Big Snit is packed with visual gags that are only on screen for a few frames, especially in scenes of panic resulting from the announcement that nuclear war has broken out.
The scenes of panic in the streets include a motorcycle driving over the cars on the road, a car seemingly being driven by a pack of dogs, a man in a turtle-drawn chariot, a telephone box being pushed along in front of a car, a man in just the back half of a car holding onto the fender of the car in front of him, a car somehow driving while upside-down, Noah's Ark (on the road, no less), a man sleeping peacefully in his bed somehow keeping pace with the cars around him, a steam engine, and a man on a hostess trolley.
A high altitude shot of nuclear missiles flying all over the world includes a shot of Santa Claus and his sleigh and reindeer - complete with the sound of jingle bells.
When the bombs hit, sending the protagonist couple (and their cat and parrot) to heaven immediately, a collection of Scrabble tiles reading "HOTEL 10 KM" floats on screen for a few frames.