The way the hyena disposes of the zebra. Same with the orangutan's fate. Pi's tone of despair is also notable, as he witnesses this feeling powerless, in great, nightmare-inducing detail.
Not to mention how Richard Parker kills the blind man.
But the man-eating trees take the cake.
Being stuck on a lifeboat for the better part of a year with a Bengal tiger.
Driven home by the movie adaptation. The tiger isn't just some cute Disney big cat; the primal, natural human fear of Panthera [tigris, leo, onca, you name it] is played for all its worth.
How about the story at the end that replaces all the animals with humans? Reading about how the humans killed each other was far more terrifying than the predatory behavior in a hyena and a tiger.
The carnivorous island. With a "fruit" that has human teeth in the center.
Not to mention that it resembles a dead body from afar. Even worse? It looks like Pi's!
The image of dozens of dead fish, swirling lifelessly in the pool.
For aquaphobics, a lot of the sea storm scenes from the movie are terrifying. Particularly when Pi swims through a slowly flooding boat to find his family, or when we see just how tiny the boat is when surrounded by enormous black waves.
Double if you are seeing it on 3D.
The tension as a young Pi sticks his hand and some meat through the bars for Richard Parker in the film adaptation.
Not to mention his dad tying up a goat and letting the tiger slaughter it for the sake of making his son watch.
The worst part of the scene? When it cuts back to the view of Richard Parker devouring the goat, the carcass is on the same side of the bars the tiger is on, but is otherwise bloodless. It's easy to assume that the noises heard during the cutaway were not just the big cat biting down repeatedly, but due to him yanking the goat through the bars and breaking several of it's bones in the process.
Also that extremely tense moment, complete with tense music, where Pi reaches a hand toward the semi-conscious and weak Richard Parker, lying on the bench. Sure, it becomes a CMOH, but Richard Parker looked like he was going to lash out.
In the film there's a brief part of Pi's hallucination that shows a hybrid of two of the most terrifying-looking underwater creatures: vampire squids and angler fish.
There's something haunting about seeing the Tsimtsum, empty and lifeless, lying on the bottom of the ocean.