The moment where Helen leaves the kids to go find her husband and Violet runs after her, because she couldn't make her powers work earlier. Helen gives her the best reassuring-parent speech a kid could ask for.
Bob whispering to Helen that he's not strong enough to lose her or the kids again… and Helen gently reminding him that she's a powerful superhero, and so are their children, and they're gonna kick ass together.
The phrasing "I'm… not strong enough…" is especially meaningful.
After 15 years of being in hiding, The Incredibles and Frozone are finally applauded as true heroes.
When Helen catches Jack-Jack in midair after his (literally) explosive tantrum following Syndrome's attempt to kidnap him, he instantly calms down and coos "Mama."
When Violet and Dash were going to be squashed on and killed by the Omnidroid, Bob rushes in to save them and tells them to go. Not a minute later, Helen literally scoops up a just woken up Violet into her arms.
"That's my girl." Cue a thousand of feels.
The look on Mr. Incredible's face the first time he sees Dash run on water.
The look on Dash's face, when he realizes he's running on water!
One from the commentary: Director Brad Bird spends nearly the entire thing singing the praises of all the animators who worked on the project, and at one point laments the fact that he probably can't name check every single person who made the movie. This is a guy who really loves his work, and the people who made it possible.