Darkseid, the Big Bad, is a stone-skinned Evil Overlord from a Crapsack World who isn't amusing or likable or suave like Lex Luthor: he's just cold, calculating, and plain evil. While the show weakened Supes so the villain of the week stood a chance, Darkseid was one of the few to really crack Supes and inflict Clothing Damage. Darkseid after he is all beat up himself isn't a pleasant sight, either.
Granny Goodness, a sadistic hag who raises orphans to be superpowered killers loyal to Darkseid through torture and brainwashing. And she's voiced by Ed Asner, of all people.
The Toyman is portrayed in the episode as completely disturbed, wearing a porcelain mask, sporting a creepy child-speak, and wielding genuinely dangerous weapons. Said weapons include a bouncy ball that gains in speed until it ricochets so fast it can crush steel, toy soldiers that fire real bullets, and "Dopey Doh" - a self-replicating biogenic weapon designed to suffocate its target. And he always seems to come out of the shadows. Even his duck-like Giant Mecha is creepy.
Fridge Horror ensues when the Toyman captures Lois Lane and dresses her up as a doll.
In the follow-up episode, he is now a Stalker with a Crush, is actually made worse in that regard, as the character named Darcy, the model, is later revealed to be a human-like robot he created as a "playmate". Lana catches Darcy removing her face and spot welding her facial circuitry to repair damage from the Toyman's latest kidnapping attempt.
The origin of Parasite: he's in the back of a truck and chemicals spill all over him, horrendously transforming him into a monster than can drain abilities and memories from other people, even Superman. At one point, he switches to Clark's voice and calls in sick for him. On a related note, Parasite's screams in "Two's a Crowd" are some of the mos unnervingly realistic ones placed into a kid's television show.
Unity, a local Eldritch Abomination that shares some similarly with Yog-Sothoth and Shub-Niggurath; not the first time that the show went to the Lovecraft well (see below). It also wasn't working alone - the Preacher depicted above? He's essentially Nyarlathotep, and reveals a One-Winged Angel form when the Supersibs directly threaten Unity. Especially horrifying during one scene where the Mind Rape portrayed is way too reminiscent of actual rape.
Karkull. In the comics, he's a guy who can turn into shadow; in the series, he's basically anotherNyarlthotepExpy. He turns the Daily Planet into a portal to elsewhere and it promptly starts spewing out shoggoths, which possess any unlucky humans that happen to be nearby including Lois Lane and Jimmy Olsen. At the end, as Superman goes to the bottom to catch the tablet that can re-seal him, a barely-perceived Outer God starts rising up to consume him. Also, when Karkull is chanting out a spell, the words he uses are real, as a literal Ominous Latin Chanting.
Metallo, a criminal who, after being jailed by Superman, agrees to be turned into a cyborg by Lex Luthor; then, after the transformation is complete, he realizes that he doesn't have any sense of touch, taste, or smell, and it drives him mad, as he's pretty much deprived of your senses and stuck in an unfeeling metal body for the rest of his life. The part when he rips off half of his fake skin is the exact moment he realizes exactly what he has become.
The Stinger at the end of the three-part pilot The Last Son of Krypton. Hapless alien explorers discover Brainiac's satellite pod after he ditched Krypton like a rat escaping a sinking ship. Brainiac then bursts out of the pod, and things get ugly very fast. He murders the aliens so brutally that we actually see their blood splatter on the walls. He is cast in shadow the entire time, which just makes it worse.
The series generally stays away from any real violence, except in one memorable incident in part two of "The Main Man", where Lobo grabs a Sandworm by the tail and rips off its skin.
In another instance from "The Main Man", Lobo is pacified by two Green-Skinned Space Babe robots who hit him with sleeping gas by folding up the entire top halves of their skulls to reveal hoses.
The ending of "The Late Mr. Kent". Detective Bowman is desperately trying to figure out why Clark Kent wasn't killed by his car bomb. In the very last scene, he finally realizes he's Superman. And then the lever to the gas chamber he is being executed in is pulled.