Rex was playing Buzz Lightyear: Attack on Zurg on a Super Nintendo Entertainment System, which is probably a reference to how the first Toy Story video game was released on it.
In some US prints, when Buzz gives his speech, it had the US flag. In some non-US prints, it had a globe with fireworks.
The toy car that Jessie rides to help Buster is the same as her previous owner Emily's as seen in her flashback, sans the wood side paneling.
Several arms belonging to other characters as seen in Woody's Nightmare.
The car that Andy's toys ride to navigate Al's Toy Barn is seen earlier as a Hotwheels-sized car being pulled out of Andy's toy box by the Green Army Men in their search for Woody's hat.
It turns out Zurg is Buzz's father, a parody on the relationship between Darth Vader and Luke Skywalker in Star Wars.
During Woody's nightmare, when he's thrown into a trash, some of the severed arms belong to Rocky Gibraltar, Rock 'em Sock 'em Robots, Emperor Zurg, Mr. Potato Head, a baby doll, and a robot.
References to Toy Story
The Buzz Lightyear: Attack on Zurg opening states that Buzz is in the Gamma Quadrant of Sector 4, which is where Buzz said he was stationed when Potato Head asked him where he was from. Also, after Buzz lands, he looks around exactly the same way he did when he "landed" on Andy's bed (breathing included) and has almost the same dialogue when talking into his wrist communicator.
Toy Story 2 intentionally reuses scenes from the original Toy Story, with many of Buzz and Woody's roles switched. The prime example of this being when Buzz is trying to convince Woody he's not a collector's item by saying "You are a TOY!" as Woody did at the Dinoco gas station.
Woody's "oof" when he falls off of Buster is the same sound he makes when the bowling ball from the closet falls on his head in the first Toy Story.
A red toolbox identical to the one Sid owned in Toy Story (minus the Binford logo) appears at the yard sale.
Woody losing his arm is similar to when Buzz lost his (although Buzz lost his left, and Woody lost his right).
Buzz inspecting the Utility Belt Buzz is done in the same fashion as when Woody first inspected Buzz in the first film.
When Zurg is fighting Utility Belt Buzz and smashing the buttons on his chest, it's done in the same way Woody was fighting Buzz, skipping the line "Buzz... Buzz... Buzz Lightyear to the rescue."
When Jessie was fighting Woody, she had him in the same position Buzz had him when they fought at the gas station.
The Pizza Planet delivery truck Woody and Buzz hitched a ride on in Toy Story was used again in Toy Story 2 by Buzz and the rest of Andy's toys to get to the airport to save Woody (Pizza Planet's trademark aliens where also seen in the car).
When Andy's toys are leaving, Buzz gives Utility Belt Buzz the same Vulcan salute he gave Woody.
Buzz opens the helmet of Utility Belt Buzz, who gasps for air, similar to when Woody opened Buzz's helmet in the first film.
Utility Belt Buzz also tackles Woody and says "Watch Yourself!" after entering Al's room much like Buzz did when he first met Woody and noticed the other toys coming.
When Mr. Potato Head tries to open the window and falls out his arms is a nod to Toy Story when he tries to lift a "weight" his arms fall off.
Both films end with a final dialogue between Woody and Buzz if they are worried about something.
The ball from Luxo, Jr. is shown in the Al's Toy Barn TV commercial. It can also be seen when Buzz Lightyear and the toys enter the toy store, and a container of those balls can be seen to the left of the door when exiting.
As Hamm flips through the TV channels looking for the Al's Toy Barn commercial, frames from several Pixar projects go by including Tin Toy, Knick Knack, Red's Dream, Luxo, Jr., Pixar's Listerine commercial and their old logo from the 1980s.
Flik and Heimlich from A Bug's Life can be seen close-up in one of the outtakes, returning the favor, after Woody made a cameo in in one of the outtakes for A Bug's Life.
Heimlich can also be seen in the actual movie, when he is crawling on a branch just before Buzz Lightyear cuts through.
Also in the same scene, the bug bar from A Bug's Life is also visible.
The cleaner who comes in to clean up Woody is Geri from the short film Geri's Game. In one of his drawers, his chess pieces can be seen.
Some merchandise from A Bug's Life can be seen in Al's Toy Barn before Buzz discovers the Buzz Lightyear aisle.
The canyon from A Bug's Life is re-used for Zurg's planet. Note: the floating rocks in the canyon were inserted by accident, but John Lasseter liked how it looked, so it was used in the final version of the film.
During the bloopers reel in the end credits, a few characters mentioned the existence of Toy Story 3. It came true 11 years later after Toy Story 2.
Toy Story 2 is the only Toy Story movie to utilize outtakes.
According to Pixar's Studio Stories: The Movie Vanishes, Oren Jacob and Galyn Susman tell the story of when someone entered a "/bin/rm -rf *" command on the Unix server that Toy Story 2 was on. This command deletes everything "as fast as it can." It made all the data disappear in front of their eyes. 20 to 30 people who worked for a really LONG time had their work erased in 20 seconds. The machine was unplugged and plugged back in. This stopped the deletion, but still, most of the film was gone. Fortunately Galyn had a copy of the movie on her home computer. The computer was carefully driven to the Pixar office and restored to the servers.
When the Barbie backpack containing Stinky Pete arrives on the conveyor belt, the announcer in the background announces the arrival of a flight named LassetAir flight A113. The LassetAir part is a refrence to director John Lasseter and A113 is the easter egg that has appeared in several Pixar films to date. However, in the DVD version, the part is misinterpreted by the subtitles as Atlantic Air flight 810.
Hamm threatening Stinky Pete with his kung fu Pork Chop is the only dialogue exchanged directly between actors John Ratzenberger (Hamm) and Kelsey Grammer (Pete), both of which are most well known for playing Cliff Clavin and Frasier Crane, respectively, on the 80s TV Series Cheers. Another Main Character of Cheers was Woody Boyd, played by Woody Harrelson.
Ironically, in A Bug's Life, Ratzenberger (as P.T. Flea) exchanged much more dialogue with David Hyde Pierce (as Slim) who plays Frasier Crane's brother, Niles, in Frasier's spin-off series. In the Season 9 episode of Frasier, "Cheerful Goodbyes", several actors from Cheers reprise their roles, which results in all three of them together for the majority of the episode.
Also, in the Frasier episodes "Momma Mia" and "Don Juan In Hell: Part Two", Frasier and Niles' mother and a look-a-like of their mother are played by Rita Wilson, Tom Hanks' wife.
Deleted Scenes
Godzilla Rex
This is another way of getting Woody into the yard sale box. It shows some of the characters getting in position for Godzilla Rex (Who is played by Rex) to come. When Godzilla Rex appears the Green Army Men "shoot" with their guns but it doesn't work. Everyone runs away from him except Buzz Lightyear has a plunge and shoots it at Godzilla Rex causing Godzilla Rex to go on a Hot Wheel car and knock over some things until he holds on to a chair making it fall on the Toddle Tots Fire Truck which Woody is on and makes Woody fly off the fire truck and goes into a window and slides his way from the roof into the box. They deleted this scene because they thought it was too coincidental. It's likely that this scene was animated during the film's direct-to-video production since in the original storyline, Woody falls into the yard sale in a much similar way.
Changed Scenes
The original animation had Al not only steal Woody but also restore and repair him on his own. However, as the story went on, it became clear that this couldn't be possible and the decision was taken to add a another character, hence the use of Geri from Geri's Game.
In the film's climax when Woody and Jessie escape from the plane via the wheel hatch, the first animation shot had Jessie slip and Woody catching her from falling. Joan Cusack, who provided the voice for Jessie, came up with the idea of having it being switched around and that Jessie saved Woody from falling off.
