This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Thief and the Cobbler
The One Eye's War Machine, not to mention the One Eyes themselves. A huge, vicious, implacable army led by a bloodthirsty, monstrous tyrant who uses slaves as furniture and only wishes to destroy everything he sees, atop a vast, disturbing war machine. Imagine what would have happened if Tack hadn't been able to stop them...
Also the sounds that the golden balls make when bouncing around in the Recobbled Cut. They're like bells of doom from hell.
The Bandits are far too ugly to actually be 100% human.
From the Recobbled cut—Tack is very-nearly eaten alive by Fido, while in a very small cell with nothing but his own ball-and-chain to try and keep the bird away.
Zig Zags death at the hands of his "friends", the One Eye's crocodiles.
The Thief almost getting his hands cut off as punishment for theft. He gets out of it by using a pair of backscratchers shaped like arms, but still. It doesn't help that this is the only time in the film despite his constant misfortunes that he gets a true Oh, Crap! expression.
The Miramax cut goes for a Nothing Is Scarier technique for the witch. She only appears as a wispy spirit, a floating eyeball, or as a swarm of bats, never showing her true form.