The thought of Bilbo going through the dark Goblin tunnels on his own, afraid of any openings in case something comes out. And Tolkien describes that not even the Goblins know what lives in the mountains. Some of the holes have their original owners still living there and other creatures have crept in.
At night in Beorn's house. Beorn tells them not to go outside. Bilbo hears him in bear form and is scared he is going to come in and kill them all. When they go out the next morning they find many bear tracks.
How close the spiders come to killing most of the company. If Bilbo had been a bit slower the spider would have wrapped him up.
Smaug's thoughts and dreams of greed and violence.
The way Gandalf announces himself to Bilbo, with lightning and a close-up of his eyes.
Far from being bumbling and slow witted like in the Peter Jackson film, the trio of trolls are actually cunning and intelligent, as they instantly pick up on the fact that if Bilbo was there, then he'd have company. Heavily implied with their last conversation, they had a pretty good idea of what they were cooking and just arguing about the method, the worst being eaten "raw". Only by Gandalf's intervention, that the company was spared.
Gollum, both in appearance and Brother Theodore's voice work. Until Andy Serkis came along and made the character his own, he was the definitive Gollum, and some fans say still the creepiest.
The goblins' first appearance when they appear to be getting closer and closer in the dark.
Some people can find the scene where the Great Goblin almost bites of Thorin's head scary.
The "Riddles in the Dark" music.
It cannot be seen, cannot be felt, cannot be heard, cannot be smelt, it lies behind stars and under hills, and empty holes it fills, it comes first and follows after, ends life, kills laughter. The answer is dark. The dark. Dark...
The 15 birds scene. Bilbo is unable to climb into the trees and turns to see the Goblins riding towards him on wolves. Dori only just helps him up as a wolf snaps at him. Then watching the Dwarves calling for help while the trees are burning beneath him.
The spiders of Mirky Wood are bat faced Ax-Crazy fiends that cocoon and then eat their victims alive, especially creepy with their big blue, pupil-less eyes.
While Smaug's appearance is silly, when he goes berserk, he is quite frightening for sure!