Toy Story (and Toy Story 2) – obvious
Bugs Life – above the City
Monsters Inc – near the trailer that Randal is banished to
Finding Nemo – seen zooming by on the street during Gill's proposed escape plan
Incredibles – in Metropolis near the end of the film
Cars – a pizza planet truck with eyes is at the stadium at the end of the film
Ratatouille – seen briefly during the paper chase
WALLE – Eve looks in one for the plant
Up – as mentioned

Toy Story (and Toy Story 2) – obvious
Bug's Life – above the City
Monsters Inc – near the trailer where Randal is banished
Finding Nemo – shooting past as Gil describes the escape plan across the street
Incredibles – On the street in Metropolis toward the end of the film
Cars – a version of the truck with eyes is a fan at the second race at the end of the film
Ratatouille – seen briefly during the paper chase
WALL-E – EVE looks in vain in a beat up one for the plant
UP – as mentioned above.

Hope that helps! Happy Pixaring!