“Brodie, err, Buddy”, i understand may have been a reference to Jason Lee’s character of Brodie from Mallrats
the aircraft Helen/Elastigirl is piloting looks vaguely like a Gulfstream IV (Steve Jobs, CEO of Pixar and Apple was given a Gulfstream IV by Apple stockholders when he returned to Apple around '97-98)
the OmniDroid 9’s blade/feet/arm/spinner thingies look sort of like Maximillian’s blades (Maximillian was the evil red robot onboard the Cygnus in Disney’s “The Black Hole”)
there seems to be a running question here, is Helen’s aircraft I.D. of India Golf Niner Niner (I.G. 99) an offhand reference to Brad Bird’s underpromoted masterpiece of animation “The Iron Giant”, which was released in 1999?
what other “unintentional” references have you found
Syndrome looks just like a caricature of Brad Bird! What a coincidence!
The Nomanisan Island security forces chase scenes were looked and sounded just like the speeder-bike sequences in Return of the Jedi. What are the odds?
When Mr. Incredible is battling the omnidroid (the first time) and it rolls up into a ball and he is running from it–very much like Indy in Raiders of the Lost Ark.