In "The Spider and The Flies", the mysterious exterminator is revealed to be a humanoid spider. Years later, Marvel would introduce Patton Parnell in Spider-Verse, who is also a humanoid spider.
In "Hunted", the hunter who is the demon creature sounds remarkably like D.C. Douglas's voice as Albert Wesker, but with a deeper voice.
"Gorilla's Paw" featured someone nearly causing the end of the world via a wish granted by an Artifact of Doom seven years before The Legend of Zelda: Majora's Mask did. Bonus points for airing a month after the NA release seven years later, and the same month as the PAL release.
The ending of "A Game Of Tag" in Zekkyou Gakkyuu has the villain be trapped in an eternal chase forever... something "The Works...In Wax" did first.
Narm: In "Cold Blood, Warm Hearts", the female lead's Big "NO!" when the captain attempts to shoot the sea monster.
The captain himself, since nearly every line out of his mouth is a sardonic laugh. The first time, it's properly intimidating. The next hundred or so times... not so much.
The continued close-ups of the captain's face when the sea monster is revealed to be a shapeshifter distract from the mood. Not helped by the fact that the captain points what looks like a cardboard tune at the monster... and he surrenders without even considering a fight.
The part where the two sea monster shapeshifters finally meet and fall in love is ruined when the camera inexplicably cuts to the unconscious captain, making it look like he fell asleep due to it.
Any time anyone mentions Pharaoh Ikamokama in "This Wraps It Up."
Nightmare Fuel: Despite the lack of gore, the show (at least the ABC seasons) did manage to be extremely unsettling, especially for a children's show.
Many of the villains were out to murder the heroes, or had killed others before.
Seasonal Rot: The CBS episodes, for being too preachy and not scary enough, thanks, in no small part, to the FCC's call to make kids' TV more educational and CBS' Standards and Practices being stricter than ABC's.
Some Anvils Need to Be Dropped: Say what you will about the third season, but some of its lessons were actually valuable. The episode "Unpopular Mechanics" had the moral that technological skill is only good when used constructively and the very loose adaptation of the comic story "Drawn and Quartered" explained how revenge against your enemies is never worth it.
Season 2's "Uncle Harry's Horrible House of Horrors" has another valuable lesson: just because you're an adult doesn't mean you can't have fun or an imagination.
"The ability to enjoy life is measured in the depth of one's imagination."
Tear Jerker: "The Weeping Woman", especially when you find out why she's weeping.
Theending. Heck, the characters in story and even the Crypt Keeper are crying at the end.