I was inspired to "hunt down" many secrets as I can in Toy Story 3 after seeing this video of some of them.
http://www.youtube.com/watch?v=4QMlMwW45x4
I'll give you some example secrets. One from a past reference, and the other as a future reference.
- Finding nemo, buzz lightyear in the dentist waiting room
- Cars, wall-e runs across in the beginning of the movie when mcqueen goes into the pit stop (came before, he may not be there when you're seeing a different copy of the movie)
Also the Pizza Planet van from Toy Story 1 appeared in most of the pixar movies. If you want to find them yourself, don't look in the white box.
Bugs Life - seen beside the trailer before flik goes into the city
Toy Story 2 - Yeah we all know that
Monsters Inc - When randall gets a beating in the trailer. It's the exact same picture from Bugs Life with the same pizza planet van.
Finding Nemo - During the escape plan from the dentist. The van goes by fast.
The Incredibles - Not in there
Cars - Somewhere in the top of the audience before the california race
ratatouille - drives across the bridge in the scene when being chased by skinner
wall-e - when eve arrives on earth. She scans the engine thing of the van
up - when the blimp was close to the ground, i think the van was there...
toy story 3 - during the story on how lotso arrived at the day care. He falls off it.