Cross-Dressing Voices: Brad Bird as Edna (they brought in Lily Tomlin to voice Edna, but when she heard Brad demonstrate the kind of voice he wanted, she immediately declared Brad needed to do the voice himself).
Enforced Method Acting: To give Dash a more realistic sounding out-of-breath voice, Brad Bird would make Spencer Fox run laps around the studio.
There was also a significantly different opening where Syndrome (then a One-Scene Wonder) was to have tried to ambush the Parrs (then referred to as the Smiths) at their house as revenge only to be killed, and the reason for adopting a secret identity as their only identity was also closer to that of Witness Protection than as the result of a law created as a means of preventing damages to property from Superhero duty as a result of complaints by the public.
Disposable Pilot: This was going to happen in an earlier version, with the pilot who flies the Incredibles to Nomanisan Island going down with the plane (the reason for that long shot of Helen watching the plane sink is because his hat was going to float up). In the end, they wrote him out almost entirely for the sake of time and story flow (giving him one sentence and a framed picture of him and Helen by a plane), and had Helen fly the plane herself.
Another villain called Xerek would be the original film's Big Bad. Xerek would have turned out to be good at the end, but he was cut because this twist was too confusing and Syndrome made for a more enjoyable villain.
All the members of the Incredible family were going to have flying powers... except Bob.
Bob was also going to have invulnerability as a part of his power, much like Superman, which would risk revealing his identity in a deleted scene where he accidentally brings a meat cleaver down on his fingers, only to dent the blade. The final Bob, however, is fully capable of being cut and bleeding (by super-fighting robots at least).
Also, if you look at the supers bios, this may be a lucky accident rather than planning, one of the supers the omni-droid had to take out for testing had the ability make himself incredibly dense, thus hard to damage. Bob also got hit by a TRAIN, and a BOMB shortly within each other in the opening without too much damage, but he still did get hurt.