The amputation. Remember, no pain killers, no sterile instruments, no antibiotics.
Made even scarier by the fact that you don't see what's going on. You see the shadows on the wall, the doctors working, Scarlett's reaction... and the terrified screaming of the soldier begging them to not cut his leg off.
The birth of Melanie's son. After barely surviving an extremely painful, difficult birth, Melanie and her newborn are put in the back of a rickety wagon that is driven through a burning city where law and order have broken down, and even after they escape Atlanta they are on the road for at least two days and nights.
The yankee soldier's murder. Think about how his face must have been after the shot. Wow. Think about all the blood on the floor and then having to drag out into the garden to bury him. Nice job to do.
There's actually a brief shot of his blood-covered face. It's not very graphic, but it isn't pleasant, either.
What he was doing before getting killed is pretty awful. You are alone at home and a creepy guy jumps out with your mother's jewelry and it's implied that he's going to rape you. Creepy.
During the scene where a dazed Scarlett is wandering through the ruins of Atlanta, the camera pulls back to reveal hundreds of dead and wounded soldiers lying on the ground (also qualifies as Tear Jerker fuel).
Bonnie's death. Mammy tells Mellie that the house has basically gone insane—Rhett shot Bonnie's pony in a rage and may have tried to shoot himself, he and Scarlett have been screaming terrible things to each other in their arguments, and both are blaming the other for letting Bonnie die. And the sight of her corpse exposed for days because her father doesn't want to bury her must be pretty unpleasant.
Scarlett finally cracking after Beau has been born, having tried to bottle up her terror and anxiety all day. She ends up sobbing for her mother in Rhett's arms.
Rhett raping Scarlett can be in equal parts rage inducing and terrifying to modern viewers. What's even worse is that Scarlett likes it.
