When Bo Peep gets taken away, the car driven by the new owner has the license plate RMRF97. it's a sort of meta-Toy Story 2 (1999) reference. It's an often repeated story that the second Toy Story film was nearly entirely lost when the main file was accidentally deleted from the main Pixar servers. This license plate references the computer command which nearly erased the movie. the Unix command "rm", with "rm -rf" standing for removing all files recursively in a given directory and without confirmation. Thankfully, a pregnant employee had a backup copy of the film on her home computer, which had to be gently driven to Pixar HQ in order to save the movie.
In the first film, after Buzz shows off what he can do, Bo declares, "I found my moving buddy." Here, when the two reunite, Bo affectionately refers to Buzz as her moving buddy.
Among the myriad items on shelves at the antique shop, Bing Bong's rocket from Inside Out (2015) and Ellie and Carl's house from Up (2009) can be seen.
Tinny from Tin Toy (1988) makes an appearance in the pinball machine, and Bo refers to him by name. Just like in the short, he has no dialogue, and only lets his instruments speak for him. Tinny was initially supposed to the be the main protagonist in Toy Story (1995) but was cut because Pixar felt it wasn't right for an old fashioned toy like Tinny to be a kid's favorite toy.
The music played on the phonograph when the dummies are introduced in the antique store is "Midnight, the Stars and You," the same song played over the final scene of the Stanley Kubrick version of The Shining (1980).