These are sound effects that were created by Skywalker Sound. They were created by either Tom Myers or Jory Brum, and they debuted in the Pixar animated short film, For the Birds (2000).
These sounds were likely made by using squeaky dog toys.
Cars (2006) (Heard once as the blue birds pass by on a power line during Mack's driving montage.)
Ratatouille (2007) (An edited variant of one of the squeaks is heard once when Remy hits the roof of Linguini's fridge as he tries to teach him how to cook while blindfolded.)
Inside Out (2015) (heard once in low volume as Riley and her family move to San Francisco.)