This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / MythBusters
The Meatman is pretty disturbing in itself, but the test it's used for— showing that a person could be crushed in a closed-dress diving suit by deep water pressure— will haunt you for a good while. Watch... if you dare.
While the catastrophic failure of a water heater is spectacular to behold, the end result of what several hundred pounds of steel propelled by superheated water is capable of doing to a house, much less any poor bastard in the flight path, is made more disturbing by the fact it's actually happened.
Of course it also quickly becomes an understated Moment of Awesome for Kari, because she stops him. She takes a moment to calm herself down, then continues with the experiment until the attending EMT pulls rank. Kari Byron, Woman Of Iron.
The high-speed camera also counts, particularly when showing anything biological. Unless it's Adam being slapped in the face, that's just plain hilarious.
There are two words guaranteed to make long-time fans cringe: "Chicken Hand": several chicken thighs sewn together to mimic a human hand — which is disturbing in itself — to test the results of an improper grip on a revolver (holding one's thumb against the cylinder gap). It nearly severed the thigh. Worse, this was based on a real incident, the results of which they see in a photo they weren't allowed to show to the camera.
Also smashing quick-frozen heads to see if they would shatter like glass (as shown in Jason X). They brought out their trusty ballistics gel again, used a similar substance for brains...and used actual human skulls. Then for even more added realism, they used pigs' heads.
They even said in the show that they couldn't show the original clip just because it was so disturbing, and had to substitute with a cheesy cartoon re-enactment.
Everything about the Underwater Car myth, especially the Inverted revisit. Just watching Adam go down with the car can be uncomfortable by itself. Imagining yourself in Adam's place, in a car that's sinking for real is some serious nightmare fuel. Taken Up to Eleven with the Turn Turtle revisit. Just watch this video of Adam detailing his experience. (Also keep in mind that Adam technically "died" in the experiment. He had to use an emergency air supply, which someone in a real-life situation wouldn't have.)
Adam has stated several times that the Inverted Underwater Car is the scariest and most dangerous stunt he's ever done, as in this particular situation, him not panicking was the only reason the test went without incident.
Likewise, Jamie's time being buried alive...and the coffin started buckling.
As stated in the "A-Z of Explosions" special, nothing. As in, when they try to blow something up and nothing happens, because this means someone has to go over and find out what went wrong and fix it, putting themselves in the potential blast radius of armed explosives.
Though it was never actually aired, during filming of the Build Team's test of decapitating heads (using goats' heads as stand-ins), Tory mentioned he found how easy decapitation is particularly disturbing.
The explosive decompression myth was proven "Busted" but as a measuring stick, they did explosively decompress an airplane and blew a huge hole out of the top of it. It gave Jamie a rude reminder of how bad something like that could be if the plane was in mid-flight.
When testing that a human voice could shatter glass, they were first doing tests with speakers and Jamie attempted to mimic the tone that the glass made to shatter it and it came out as this frightening, metallic noise. Adam said he had a nightmare with this kind of noise in it once.
The "bomb baby" DIY bomb robot that Jamie built for the "Fire in the Hole" myth. I mean, look at the thing!
Jamie's "Lawnmower from Hell". So over-the-top crazy that it actually sheared its own blade off before they could get the high-spectacle ending they wanted. When was the last time that happened?
Jamie seems to be the Butt Monkey of the final season opening shorts, but some of them get downright disturbing considering the program's demographic. The worst offender has to be the one where it implies Adam accidentally crushes Jamie in a car crusher.