This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Incredibles
"I'm sorry. I've been a lousy father, blind to what I have."
The realistic "parent fighting" scene. The looks on Dash and Violet's faces after their parents know that their kids heard them. It's especially hard to watch for those who grew up witnessing parental arguments.
"Does this mean we have to move again?" is teary to the eyes for anyone who had to move a lot as a kid.
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 more so 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.
For a brief second after he hears Helen's "I love you", Bob just kind of stops in confusion. He can tell something is off, but doesn't know why, especially since to him, everything is going perfectly. Including and especially his relationship with Helen. She thinks he's having an affair, but he thinks he's actually giving his family the life they've deserved for the first time in more than a decade - doing a version of what he loves, no less.
When Mr. Incredible learns 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. Incredible; 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. Really, how could anyone see Syndrome as a sympathetic character after that?
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..." And then he sees that Frozone, who is in the same city, has his location verified...
It's even worse when you saw the second disk of the DVD and saw the superhero files. If you do that, then rewatch the scene, you start recognizing those pictures. You've read their dossiers, listened to their recordings, probably learnt everything about them. Those faces will have names, stories, personalities. Who doesn't experience the same shock that Bob does?
The scene on the plane when Helen 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!!" and Violet's face as she tries in vain to.
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 has to explain the difference between fictional 'villains' and men who'd murder a child. She really doesn't want to shatter her kids' expectations like that, but they have to know.
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.
And just look at him afterwards when Mirage comes in to free him. For a few seconds, he's so broken that his first instinct is to strangle her.
And when Bob reveals to Helen just why he'd prefer to take on the Omnidroid alone, as a direct result of the above.
Bob: I CAN'T LOSE YOU AGAIN! ...I can't. Not again. I'm not... strong enough.
The look on Helen's face when he says it implies that he's never shown this kind of fear before— but of course he hasn't. He's the Superman of his world, the strongest hero who ever lived. He can act cocky because a part of him knows that he'll always be able to save everyone. And then he got beaten down like a helpless child by a weaker version of the monster his family is about to confront. He no longer has the confidence that he'll be able to protect them.
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.
The sheer desperation in Helen's voice as she screams "Bob, throw me!!"
Worse yet, we also learn through the DVD extras that Thunderhead isn't simply dim but notably mentally disabled; he didn't graduate school, can barely read, has severe problems focusing, and even more difficulty expressing himself. He was a kind man and an incredibly powerful superhero, let down by a society that had no idea how to help people like him, especially since going by the setting he was probably in school sometime between 1930 and 1940 (having perished in 1958).
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.
It gets worse. Look closely, and you'll see that smoke is coming out of the plane engine before Stratogale gets caught in it. That means that she was in the middle of saving that plane from crashing. It's very likely that her body getting sliced up by the turbines just made the damage worse. In fact, with the exception of Thunderhead, who successfully redirected the missile's flight path, most of the supers who died because of their capes never got to save anyone calling for help.
Her cause of death is listed as suit malfunction. That hilarious "no capes" rant suddenly becomes the most depressing thing in the world.
On that note, how do you think Edna feels about all this? She designed those outfits. All of them. And all of them led to the wearers dying (or in Splashdown's case, going missing). This causes her vehement refusal to give Bob a cape and her statement that she "never looks back" to take on a much darker meaning...
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.
Bob's job woes can hit the viewer right in the gut because how many of us in our lives have tried to do good at our jobs, only to be held back by some jerk manager? Bob just looks completely broken and tired when he gets called into the meeting, barely mustering the strength to speak. This is one of the greatest superheroes who ever lived, and all it took was a crappy 9-to-5 to break him. It's summed up perfectly (and somewhat humerously) in his exchange after he's fired.
Bob (notices Staring Kid as he gets out of his car): Well, what are you waiting for? Staring Kid: I don't know, something amazing, I guess. Bob (Sighs dejectedly): Me too, kid...
The scene where Bob is getting yelled at by said boss. He happens to look to the right where he sees a man being attacked in an alley. Every part of him just wants to burst out of the building and save him like a normal hero would. However, his boss's callous reaction and threat to fire him forces him to stay and watch the attacker walk away. For a superhero, that must have killed him, knowing that he could have saved someone, but couldn't.
Think about the story from Violet's point of view. All her life, she's had to hide her powers from the world, is it any wonder she's such a Shrinking Violet for most of the film?
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.
Also, Brad Bird's commentary on the scene, which happened to be recorded the day after Thomas' death.