This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Pirate Latitudes
Cazalla just in general. A character, whose driving force in his life is his desire to inflict as much torment and agony on others as possible, and does so completely without hesitating. Even his Offscreen Villainy is pretty scary, and the fact that he is actually on the side of law, makes it even worse.
Cazalla murdering a young crewmember, for not telling him where they are heading. Makes for hell of a Kick the Dog moment, especially because he spiced it up with some Faux Affably Evil behaviour as well.
The torture of a crewmember, using rats. More specifically, he smears the hapless crewman's face with cheese, baiting the rats into eating his face. And the frightened crewman even told Cazalla what he wanted to know.
Somewhat subverted, in that while the crewman told Cazalla what Hunter was planning, but Cazalla didn't believe him. It's only after tracking the route of Hunter's departure after his escape that Cazalla realizes that yes, Hunter really was going after Mantanceros.
His Offscreen Villainy as well. He tortured and murdered Don Diego's son, for a crime the latter wasn't even guilty of. Don Diego's description of the torture his son was put through paints Cazalla as a frightening figure long before we meet him.
And finally, His Villainous Breakdown near his death, where he jumps around like a rambcouosly insane madman, after his plans has fallen apart, before Hunter kills him.
Some of the experiences at Matanceros. Climbing the Cliffs of Insanity, during a vast thunder storm, stands out, along with the coral snake crawling in the trousers of Lazue. That is especially unnerving for ophidophobes.
The Cannibal Tribe at Boca del Dragon. The islands they land at, is described as excessively weird, and you and the characters know something is awry, they just don't know quite what. They even visit what must be considered a ghost town, and finds the crocodile hide in the church, and realizes that it is the Caribs. And then Lady Almont is kidnapped by them.....