When Woody is trapped in a milk crate, he hides under a book. The book is TM-31-210 Improvised Munition Handbook. A US Army manual detailing how to make explosives/weapons/traps from ordinary household materials. Gives another look at just how warped Sid is.
The carpet design used in Sid's house is the same design used in the hotel featured in The Shining (1980).
The toolbox in Sid's room is labelled "Binford". That is the name of the tool company on Tim Allen (the voice of Buzz)'s show, Home Improvement .
The number A113 has appeared in every Pixar film (not the shorts). In this film, as well as its sequel, it is the license plate number on Andy's mom's mini-van.
After the "Hey Hamm, I'm Picasso" gag, Mr. Potato Head says to a toy hockey puck, "What are you looking at, you hockey puck?" As an insult comic, Don Rickles (who voices Potato Head) was famous for calling people a "hockey puck" in his routines.
The "Hidden Mickey" is the watch clock in Andy's room.
There are many books behind Woody when he is giving his speech and some of them are Pixar short films such as Red's Dream, Knick Knack, and Tin Toy. The Tin Toy book even has director John Lasseter's last name on it.
While Buzz is watching the commercial for Buzz Lightyear, the sound made by Buzz's laser is the same as the sound from the original Star Wars TIE fighters.
All of the characters eye blink independently, rather than together - a quirk the artists intentionally incorporated.
When Buzz & Woody are on RC, it very briefly shows Andy's little sister in the car, watching them from the mirror. In the background, we can hear "Hakuna Matata" from Disney's "The Lion King" playing on the radio.