The Hotel Cabal episode, which ends with Mace Malone frantically trying to find an exit to the sealed maze of traps, all of which are designed to drive the prisoner insane. Word of God is he eventually died of dehydration.
Demona happily destroying human statues in "City of Stone" — especially when she only destroyed the arms of one.
The 11th-century flashbacks, in which Demona becomes gaunt and aged, make her look more like a vampire than a gargoyle: and she's quite enthusiastic with that spiked mace of hers.
The Xanatos Goon Squad in "Monsters" being dragged down in their submarine to a watery grave by some very angry plesiosaurs.
Jackal in "The Green" fantasizing about smashing stone Gargoyles by day. Frightening enough as it is, but then he whips out a chisel and carves Goliath's face to look like his.
His entire killing spree in Grief. How bad is it? He starts small — a tree withers away, a couple of machines are turned to scrap metal, and a pair of Nile crocodiles are reduced to skeletons. The last thing we see him do? He lays waste to an entire thriving city!
The whole concept of Thailog, once you think about it. The guy has Goliath's strength, wordy knowledge, and combat skill coupled with the knowledge and manipulative genius of Xanatos and the scientific knowledge and goofiness of Sevarius, but without a trace of any kind of morality.
The werefox, to say nothing of Fox's transformation, especially when she's reaching out to Xanatos and screaming before the beast takes over.
The episode that first introduced Coyote was often skipped in syndication, probably because of the scene in which Bronx knocks Coyote to the deck and mauls his head. It just barely gets past the radar due to Coyote being a machine, but it's still rather brutal - and a first-time viewer would probably still assume that Xanatos was the guy in the armor.
The gang's fates in "Future Tense." Broadway gets blinded in a fight before being shot dead while Bluestone, Bronx, Claw, Angela, Brooklyn and Demona are all vaporized on-screen. Xanatos also kills his own son with a smile on his face.
The Goliath Chronicles episode "Genesis Undone" stands out as rather horrifying. The deterioration of the Manhattan clan clones is unsettling to say the least. We then get to watch as they all ( including Thailog) writhe in agony before turning to stone, at night.