The Chimera (a hideous amalgamation of a lion, a goat and a dragon)
Cerberus (a vicious three-headed dog that in some myths had a back covered in living serpents)
Orthrus (Cerberus's two-headed, serpent-tailed little brother), and various other creatures definitely count.
Perhaps the worst is Typhon — father of the above along with the Mother of All Monsters, Echidna — Typhon is described by some writers as being as tall as the sky itself, and having a hundred dragon-like heads, all of which screamed and breathed fire. It's not hard to see why almost all the gods had a collective Brown Note when he appeared, and fled Greece, leaving Zeus to face the creature by himself.
And then there's creatures like Scylla and, even worse, Charybdis, once beautiful women turned into eldritch things of pure horror. Scylla we at least know is horrifying to observe, looking like a giant, beautiful women from the waist up, with a scaled tail below, and the heads of six, rapid wolves snapping at her waist.
Medusa, whose face was apparently so frightening that anyone who saw her turned into stone.
Prometheus' fate of being chained to a rock and having an eagle peck out his liver each day. He endured it for hundreds of years before being released.
Similarly the fate Cheiron the centaur faced before he sold his immortality: living forever, with the maddening poison of the Hydra eternally burning through his veins.
The fate of mortals unfortunate enough to piss off the Olympians.
So, you're friends with Aphrodite, and she want to marry you, eldest son of Nereus, old man of the sea. That's good, right? Well, Dad says no. You tell your girlfriend that, and even though it's not your fault, she turns you into a polyp.
Many gods of the Pantheon were terrifying in the same way as Anthony from "It's a Good Life"; by marrying incredible power to a complete lack of temperance or discipline. Even the mightiest of gods could be vain, petty, selfish, lecherous, vindictive, and very enthusiastic when it came to Disproportionate Retribution. And, unlike the deities of most other belief systems who get the same accusations from time to time, this was not a matter of Alternate Character Interpretation; according to their own believers, these gods were a bunch of cruel, vicious, spoiled children and humanity was just one of their playthings.
The few tales of cannibalism (such as Tantalus and Atreus).
Zeus makes another woman pregnant, then hides her underground. She gives birth to a giant...dying of childbirth.
The same giant flirts with Artemis. He gets sent off to Tartarus to be forever eaten alive by eagles. This was not Prometheus, just some Casanova Wannabe.
Ephilatus and Otus tried invading Olympus. They eternally drown in the center of a waterfall, tied by snakes to a pillar, while Fate watches them as an owl. Ouch.
Some of the bandits whom Theseus defeated were known for their exceedingly barbaric cruelty such as Procrustes, who tied his victims to a bed and chopped body parts if they did not fit. Sinis was also pretty horrific: he bent down two pine trees with his great strength, tied the hands of passer-bys to the tips of the two trees, and then let go.
The minotaur's young victims were imprisoned in the labyrinth and force to run for their lives until the beast catches and devours them or they drop dead of exhaustion, hunger and thirst. It's like the first teen slasher flick.
The future Olympians were able to live and grow in Kronos's stomach how exactly? Squick indeed.
Antaeus the giant who was building a temple using human skulls.
The fate of the few mortals sent to Tartarus:
Ixion - bound to an ever spinning flaming wheel.
Sisyphus - forced to roll a boulder up a hill only for it to roll back down.
Tantalus - chained to a pool from which he can never drink because the water recedes. There are fruit trees whose branches he can't reach because the breeze blows them away.
The reason Ixion was there? He was invited to the Olympus for dinner and started creepily and obviously flirting with Hera. To get proof, Zeus made a cloud copy of Hera and made sure Ixion could find the cloud copy easily (while hiding the real Hera.) Ixion promptly attempts to rape the copy. Zeus, waiting only for the chance to catch him in the act, struck him dead and prepared the above-described punishment.
The reason Sisyphus got punished? Back then, Thanatos, the god of Death, actually knocked on your doors visibly and in person, so when he came to Sisyphus, Sisyphus knocked him out and tied him up, causing nobody on Earth to die. Ares noticed that though there was enough mangling and bloodshed going on on his favourite battlefields, nobody died, which put a bummer on the whole thing for him so he went to look Thanatos. After finding him under Sisyphus' bed, he freed Thanatos and the two of them killed Sisyphus then and there. In the Underworld, Sisyphus started whining to Hades about how his wife had no time for proper burial rites and how without them he could never really enter the afterlife, so Hades let him back to the world of the living to arrange things, but he told his wife not to complete the rites and stayed on as a ghost. After a while, when it was obvious Sisyphus was not planning on going back, Hades fetched him himself and put him to the task described above.
Oedipus: imagine marrying your own mother and unknowingly having intercourse with her! Horrible! Then, to the top it off: Oedipus gouged his own eyes out after he discovered all this.
King Diomedes who fed humans to his flesh eating horses, then in a Karmic Death and/or Ironic Death twist was fed to them himself.
Icarus, plummiting to his death after the wax of his wings melted from the heat of the sun.
Athena's birth. The clanging produced when Metis forged Athena's armor gave Zeus a massive headache, and he was willing to do anything to stop the headache...ANYTHING, including go to one of his least favorite people in the world, Hephaestus, and have him split his skull wide open. Then, Athena burst out of Zeus' bleeding skull, fully grown and armored, and letting out a battle cry.
And her mother, Metis, was fated to give birth to a son more powerful than Zeus. So he turns her into a fly and swallows her whole.
One woman seduced a king, and his wife organized for the other woman's children to be killed. But the seducer changed the clothes, and the queen murdered her own kids. And when the two were discovered, they were tossed off a cliff and became sea gods.