"I can't lose you again. I can't. Not again. I'm not s-strong enough."
The list of supers killed, lured to their deaths during the Omnidroid testing. Especially when you consider that these are people Mr. Incredible knew personally; look closely, and you can see most of them at the wedding. The increasing horror on Mr. Incredible's face certainly doesn't help either.
It's even more chilling if you remember from the start of the movie that all of the supers are simply trying to live as normal folk and during the dinner scene where Mr. Incredible is reading the newspaper, we see that the recent missing person used to be a super. We see him later as a corpse in a cavern.
Even worse, many of those people must have gone through the exact same arc as Bob did. Feeling unfulfilled with normal life, the supers were approached by Mirage, given a mission, kept coming back, felt good about themselves again...and then they were killed by the ever-evolving droid.
Some supers manage to beat the Omnidroid, only to be later killed by an upgraded version; however, it was actually the majority that didn't get such luck.
And Bob is quickly relieved to know that Syndrome doesn't know where Helen is. And then he finds out that Syndrome knows where Frozone is. Technically, he would've been the one Mirage approached to fight the Omnidroid instead of Bob if she hadn't noticed Bob, so thankfully, he dodged the bullet.
Also, Syndrome's death by jet turbine was just so horribly gruesome to think about.
This was foreshadowed by the exact same thing happening to a good Super. While she was waving at a child in the airplane. The special features note that she was a teenager.
Stratogale, the super hero dragged through the plane turbine by her cape, is dragged through head first! Syndrome does have time to feel something because he is sucked into the turbine feet first.
The split second before Syndrome is sucked into the turbine, there is brief shot of his face. The look on his face is pure terror.
The Electric Torture was rather disturbing, especially for something in a PG-rated movie. Made even worse in that Syndrome's expressed motive for it (the victim "sending out a distress signal") is something the victim did entirely by accident in the first place; Mr. Incredible wasn't even aware of the homing device and when he tried to tell Syndrome this, it was immediately dismissed as lying.
*Rotate* Danger *Whiirrrrr!!*
How Mr Incredible came to be caught beforehand - having dozens of unremovable black "balloons" fired at him as he struggles to escape, which expand and completely engulf the protagonist. The point-of-view shot of Mr Incredible's quickly-fading vision is chilling, especially for anyone with a fear of confinement or suffocation.
And the last thing he sees is Mirage, and we can tell from her pose that Bob is in big trouble.
For the aeronautically-inclined, hearing Helen's voice-overs as the missiles approach and ultimately destroy the plane is pretty scary, especially if you imagine hearing it over a black box.
Helen: Abort, abort! There are children aboard, say again, there are children on board this plane!
After the battle with the robot, Elastigirl is checking voicemails, and hears the babysitter that Violet hired to watch Jack-Jack panicking over the phone about her infant son. Just when it comes to a head, the girl calms down and thanks her for calling a replacement sitter. The full force of the moment floats right over the heads of younger viewers, but the look of abject horror on Bob and Helen's faces and Helen's frantic, "I didn't call a replacement!" is terrifying to older audience members.
Of course, we do see that Syndrome just had to show up and claim he was the replacement babysitter without having to prove anything.
"I mean, after all, I am your biggest fan."
"He's getting away, Bob! We have to do something, we have to do something now!"
In the alternate opening on the deleted scenes, there's this really creepy moment after Syndrome hears baby Violet crying and then says to Bob, "You are breaking the law, Mr. Incredible. You know supers aren't supposed to breed," his eyes just slowly move in the direction of Violet's room. There's something very unsettling about that moment which cranks up Adult Fear to the extreme. Syndrome has Bob and Helen trapped with his freeze ray and there's nothing they can do to stop Syndrome as he moves down the hall toward Violet.
The fact that people with superpowers were legally unable to have any kids is pretty uncomfortable to think about in and of itself.
The scene of the man getting mugged, and the scene of the man attempting suicide at the beginning. Both realistic scenes.