The effect that the alien fluid has on Wikus. Most of the Nightmare Fuel in this movie runs on the Body Horror of Wikus transforming into a prawn.
First, there's the vomiting, which is gross, but not necessarily horrifying. But then he starts hacking up black liquid, which sends him to the hospital and then that's when he discovers that his hand is turning into a prawn claw. And as the movie progresses, it gets worse, and then at the end, as Tania is being interviewed she shows the metal flower that was left at her door and then there's a cut to Wikus fully transformed into a prawn, making the flower in District 9. The fact that he still can remember his wife, and not knowing whether or not Cristopher will return to reverse the transformation or if it can even be reversed is unsettling.
What was just as horrifying was the scene at the party, in which Wikus spews black liquid onto the cake, and then reaches in his delirium for the paper towels to start futilely mopping it up. That small, subtle gesture represented a last desperate gasp at clinging to normalcy, an attempt to put off just a little longer the horrible Body Horror and Transformation Trauma that would characterize and shape the rest of the film. The way time stops and slows to draw attention to the precise last moment before reality irrevocably breaks is simultaneously terrifying and heart wrenching.
After Wikus's alien arm is first discovered in the hospital and he's forced into what is basically a body bag for transportation to MNU while still alive and fully conscious is pretty damn terrifying in its own right
The MNU doctors attempting to dissect Wikus, live and fully conscious. Not that they managed to do it in the end, but the fact he was one of them, he worked there and they were willing to do it so unquestioningly. Plus his father-in-law just ignoring him.
And let's not neglect to mention the scenes where Wikus is basically being tortured in the MNU hospital room.
The worst bit for him may have been the scene when they're getting him to test out the guns and they walk out a live prawn in front of him. What was even more awful was the fact that they kept on electrocuting him even after he agreed to cooperate.
The scene where Wikus is scarfing catfood (which is pretty disturbing in itself) then he chokes and suddenly spits out a few molars.
When Wikus tries to cut his alien claw-hand off, but instead just cuts off one of the alien digits. The pain is so great, Wikus then starts to drop the Cluster Fock Bomb.
Wikus's growing exoskeleton puncturing his flesh from the inside, causing it to bleed, and causing excruciating pain for Wikus.
How can we forget the scene when Wikus cheerfully takes a flamethrower to a nest of prawn eggs? The prawn babies are still alive. And they're screaming in pain as they're burnt. And if that weren't enough, what really did it for me was how Wikus cheerfully explains to the camera what they're doing, and then compares the popping sound it's making to popcorn.
In the scene where Wikus is out evicting aliens, Wikus is trying to lure out Christopher's child to be taken away, saying to his son "It's the Sweety-Man..."