A behind-the-scenes example has to go to Holly Hunter for actually learning what the radio protocol for pilots actually meant. The result... an intense nail-bititng scene that doesn't feel scripted or acted, which for an animated film is truly mind-blowing.
Elastigirl knocking Mirage out for the count. Yes, she did it under a wrong assumption, but knowing what Elastigirl thinks is going on is enough to see it from her side. Plus, I laugh at Mirage's expression every time. Elastigirl must have one hell of a punch.
The fights on the island:
Mr. Incredible gets his groove back.
Elastigirl infiltrates the base and rescues her husband without being noticed at all.
Dash and Violet using their powers professionally for the first time and learning that, yes, they're super, and they can hold their own against fully grown bad guys.
After thinking his family was murdered by Syndrome, Mr. Incredible threatens to kill Mirage. Later when she tends to him we see he's a clearly broken man with nothing left to lose, so he grabs her by the throat like he's going to choke her to death, demanding what else they can do to him.
Actually, judging by Bob's grip and how Mirage's head changes shape abit under the pressure, it's more likely Bob threatened to crush her skull, and that choking was more of a side-effect.
Mirage calling out Syndrome over him not trying to save her, leading to her Heel Face Turn.