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Nightmare Fuel: Treasure Planet
As soon as you see Scroop with the rest of the crew, you just KNOW he's the one you really do not want to be alone with.
While we're on the subject of Scroop, on the ship when Jim steps out to shoot at Scroop, the lights suddenly go out, courtesy of B.E.N., who is trying to disable the laser cannons, and the emergency lights turn on, revealing Scroop has disappeared. As Jim looks around, Scroop appears above him about to strike.
In a subtler way, the revelation that Silver is planning treachery (along with either murder or a mass marooning) makes his pleasant behavior quite chilling.
The confrontation between Jim and Silver after Jim overhears the mutiny. As they're both speaking, Silver turns his mechanical arm into a pistol behind his back, obviously intending to shoot Jim.
However given how he stopped from shooting Jim when he (along with Captain Amelia and Doppler) were about to escape, it's likely he was just going to scare Jim and/or take him as a prisoner.
When Scroop is sent flying into space. At first, it seems like no big deal, until you realize he's trapped in space until he dies of dehydration. The look of terror on his face makes it worse.
Mr. Arrow's death scene.
Hell, what about the goddamn BLACK HOLE?! That entire scene was terrifying!
The fact that Jim was so close to falling and could have died a horrible death of being burned alive by the planet's core.