The realistic "parent fighting" scene. The looks on Dash and Violet' s faces after their parents know that their kids heard them.
"Does this mean we have to move again?" for some reason is teary to the eyes.
Mr. Incredible in his room pondering whether or not to take the mission, and seeing all the memorabilia of things he has accomplished throughout his superheroic career just makes your heart drop at how much he's done.
When Helen listens in on the phone call between Bob and Mirage, and assumes them to be having an affair, the look on her face when she says "I love you, so much." is heartbreaking.
Even moreso when you take in Bob's casual attitude towards her as he goes off to "work"— from her perspective, he's brushing her off because he's got someone new, but from his perspective, everything is just hunky-dory as usual.
When Mr. Incredible learned the totality of Syndrome's plan via computer.
Especially when you remember that all the supers who died perfecting the Omnidroid weren't just allies of Mr. Incredibles; they were his friends. Several of them had been at his wedding, and he recognized Gazerbeam instantly upon seeing the picture of his secret identity in the paper. Also remember that each of the supers had gotten the exact same message as Mr. Incredible, reminding them of their Glory Days, asking them to come back and make a difference one last time...and leading them to be unceremoniously slaughtered to perfect a machine that will be used to discredit supers once and for all.
Look at his face when he sees that Helen's whereabouts are listed as unknown. That is some serious "Oh thank God, she's safe, they don't know where she is, she's safe..."
The scene on the plane when Helen aka Elastigirl realizes that Syndrome's missiles are going to hit them and they cannot be stopped, all the while frantically yelling "Abort abort abort! There are children on board!" into the radio. Her face shows pure terror. She then unhesitatingly leaps into the back of the plane at the last second, fully prepared to die for her son and daughter.
"Put a field around us NOW!!" There is something about that line that's heartstring-tuggy for an unknown reason.
Violet's face when she tries to do a force field is upsetting. She's trying so hard and she just can't do it...
And later, when Helen leaves Dash and Violet in the cave, Violet runs out after her and tearfully apologizes for this.
Mirage's expression of pure horror upon hearing "There are children on board!" from the receiver signifies one thing: Her boss has deliberately sent missiles to shoot down a plane which has now just been discovered to have children on board, and even with this new information he still doesn't call them off. A mother and her children are going to die and Bob and Mirage are unable to do anything but listen to the inevitable explosion.
In one of the deleted scenes (only storyboarded), the guy Helen gets the plane from actually goes with the family. When Syndrome blows them up, he doesn't survive.
Helen telling her children that they won't be spared because they're children.
Bob initially believes his family has been killed. Syndrome's Kick the Dog line about working alone only makes things worse. You can even hear him weeping bitterly in the background as Syndrome walks away, it's heartbreaking.
Syndrome's 'reason why I did it' speech. It just sounded so much like he was still that disillusioned kid, and who doesn't remember how much those kinds of disillusions hurt?
It's very brief but during the fight with the Omnidroid, Dash tells his father to throw Syndrome's remote and Bob does. While he's running for the remote, we can see Helen. The look on her face is heart wrenching; just imagine having to watch one of your children, who's only about 9 or 10, being attacked by a machine whose purpose is to kill people like you and your child. And the way she reaches out her arms to her son, but he's too fast....No parent should have to go through that.
Syndrome's attempted kidnapping of Jack-Jack. He freezes all of them so that they're helpless to stop him gloating about how he's taking away their future, then blows a hole through their roof to escape. After he takes off, Jack-Jack wakes up and immediately starts crying in terror. It's made even worse by the terror on all their frozen faces, and when they try stopping him getting away they can't, for fear that they'll kill their baby son.
Stratogale was still in high school when she got sucked into that airplane engine.
A bird can cause the airplane engine to malfunction, Stratogale is a Flying Brick...............those kids she was waving at and everyone else on the plane, they're dead or went through what will likely be the two most psychologically scarring events of their lives in one go.
Her cause of death is listed as suit malfunction. That hilarious "no capes" rant suddenly becomes the most depressing thing in the world.
Bob's work at his job - being stuck at an insurance company that refuses to insure people who desperately need (and legally deserve) the money, topped off by a cruel, selfish boss who yells at Bob for doing his job. There's also the implication that he doesn't discuss this with Helen at all, as she's under the impression that he "helps people" for a living.
This one is more a tear jerker with backstory- when the Omnidroid is defeated, two old men look on and say "You see that, Frank? That's how you do it, that's old school!" "Yeah, no school like the old school!" Nothing heart wrenching about that, but consider that they were voiced and modeled after Frank Thomas and Ollie Johnston, the last remaining members of Walt Disney's Nine Old Men group of animators. Frank died a couple months before The Incredibles premiered, and Ollie Johnston died in 2008. "No school like the old school" is an incredibly poignant tribute to old school men such as them and with both of them gone it makes me cry every time I see it.
Also, Brad Bird's commentary on the scene, which happened to be recorded the day after Thomas' death.