Indiana Jones' traitorous companion Satipo having several tarantulas on his back, which Jones casually pushes off his body, at least for the severely arachnophobic. Doubly so with Alfred Molina's description of filming the scene. He was covered with actual tarantulas, but to Spielberg's frustration they wouldn't move and looked fake. Then someone realized they were all male and added a female one, instantly causing all hell to break loose all over his body. And keep in mind this was his first movie role.
When Indy triggers one of the traps in the cave, spikes suddenly emerge carrying the decaying body of one of his older competitors. Most disturbing is the way its head fell into Indy's direction.
Indy: Forrestal.
Later, Satipo gets impaled upon the booby trap Indy and he managed to escape from earlier. His horrified expression makes it even more unnerving.
Indy:(grabs the idol) Adios, Satipo.
Major Toht threatening to burn Marion with a poker in The Raven bar. Heck, everything with Toht is terrifying due to the Gestapo Reality Subtext that surrounds him, and the actor's extremely creepy performance.
Toht: Fraulein Ravenwood, let me show you what I am used to...
The unsettling shot of the dead monkey after she ate the poisoned date palm fruits. And a second before that, something about Indy tossing the poisoned date up into the air, complete with slow-motion, shadow on the wall... and then Sallah suddenly grabbing it, face stricken. The dim lighting of the room doesn't help.
The Well of Souls is this trope both for the audience and Indy. Unbelievable numbers of snakes. And mummies. And snakes slithering out of the mummies. GAH. Imagine falling down into the Snake Pit and landing directly near your worst fears and it is ready to attack you along with the other snakes all around you. This was enough to cause Indy to panic. "Why Did It Have to Be Snakes?" indeed. And it's not just blind phobia (though Indy certainly has that, too). At least some of those snakes are cobras or asps (“Very dangerous.”), and probably others are venomous enough to be a very real lethal danger to a healthy adult human.
After Indy and Marion found a way to escape from being trapped in the Well of Souls, they are met with an awful surprise when they stumble into a room filled with decaying corpses. The corpses seem to be screeching at Marion and whenever she knocks down the corpses they fall in such a way that makes it look like they are trying to grab her.
The Giant Mook Indy fights on the airstrip is chopped up by one of the plane's propellers and while it happens off-screen, the copious amounts of blood on-screen are jarring, considering the Ark scene aside, the film is rather light on blood. It's never made clear, but in the long shot of the plane shortly before it explodes, a large smear across the sand with some chunky bits is seen near the plane...
While the Ark is being transported, it makes an eerie hum before it burns the Hakenkreuz swastika on the box it's being held in. The buildup of that moment showed several mice wandering in the ship's hold. Just before the Hakenkreuz is burned away, one of the mice rolls over and starts hyperventilating (or possibly bowing to an unseen presence), strongly implying that something had actually come down into the ship's hold for a visit.
Ben Burtt, who ironically used more “organic” sounds for Star Wars, used a synthesizer for the otherworldly hum in this scene.
To top it off, this is the first unambiguously supernatural event to take place. The power of God is not something to be taken lightly.
On top of the visual horror, the sound of Dietrich's head imploding. You can hear his brain matter turn to goop and his bones crunching! To further add to the nightmare fuel, there's the horrific hissing sound Toht's boiling blood makes, coupled with his screams getting muffled by the gurgling of his mouth filling with blood. And those screams continue as he becomes skeletonized. Even worse, when Belloq's head explodes, you can see his eyeballs fly out of the remains of his skull and brain! Sweet dreams...
Shutting one’s eyes while still hearing the flesh melting is quite terrifying.
Not to mention the rest of the Nazis dying by the lightning bolt going straight through them. Some going into their eyes!
Even before then, several of the Ark's spirits single out certain Nazi mooks for "special treatment." One is hovered off the ground as the spirit tortures him while another cowers in fear as the spirit appears to sink into the man's body and head, possibly giving him a taste of Mind Rape before he dies.
The most shocking bit? The movie is still rated PG. (Granted, the PG-13 rating hadn't been developed yet—and this film is likely one of the reasons it was developed.)
The FX crew had to superimpose fire on the shot of Belloq’s head exploding in order to avoid an R rating.
Probably the thing most overlooked is that it's more or less a confirmation that within the Indiana Jones world, God exists. And we get to see firsthand what happens when He encounters a group of people who not only opened the Ark and looked inside of it, but whose agenda involved exterminating His believers.
Indy warning Marion to close her eyes and keep them shut. Whether out of reverence to God, because he knows what they might see would traumatize them for the rest of their lives… or because he doesn't want himself or Marion to watch as the spirits kill both of them, it obvious that he's terrified of what's happening.
Belloq's death in the novelization was far more brutal than in the film. His eyes would burn out of their sockets alongside his body decaying before being Reduced to Dust.
