The Well of Souls is this trope both for the audience and Indy. Unbelievable amounts 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.
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. It also doesn't help that there are screeching sounds as if the dead were screaming at Marion and whenever she knocks down the corpses they fall in such a way that it looked like they were trying to grab her.
While the Ark is being transported, it makes a eerie hum before it burns the swastika on the box it's being held in. Considering what it does in the finale, what else can the Ark do with its lid on?
Even worse, the buildup of that moment showed several mice wandering in the ship's hold. Just before the swastika is burned away, one of the mice rolls over and starts hyperventilating, strongly implying that something had actually come down into the ship's hold for a visit.
The novelization states that the mice can detect that something is terribly wrong about that specific crate. They don't know what it is, but they do know that it represents incredible danger and scurry away as fast as they can.
The moment the spirits that emerge from the Ark turn hostile is utterly nightmarish. At first, they're serene - even beautiful, as Belloq declares - and then they suddenly start to shift into skull-face terrors, snarling at those daring to look upon the open Ark. The shift in the music at this point is also rather frightening.
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. Sweet dreams...
Of all the things to remain in Area 51, the Ark is the only one that should be there. If you ever read the Bible or listened to Indy's warning, it's made pretty clear that you should NEVER OPEN THE ARK!
Earlier in the film, a Giant Mook is chopped up by the propeller of an airplane 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...