1) From "He-Man and the Masters of the Universe", check out the "House of Shokoti" 2 Parter. I watched this every year for Halloween, moreso than The Great Pumpkin special. It deals with He-Man and friends' search for an evil temple belonging to an ancient evil sorceress named Shokoti. There are monsters aplenty, good scares for small children, and some creepy villains (including Lord Masque in Part 1, who looks like a He-Man-ized version of Darth Vader).
2) Also from "He-Man: MOTU" is "Reign of the Monster" where Skeletor unleashes an ancient creature named Molkrum. I am recommending this one purely for the monster. Molkrum is one of the craziest designs I have ever seen.
3) From "Thundercats", there is "The Ghost Warrior" which was my favorite episode of the series when I was a kid. Not only does it contribute a lot to the series mythos and is essential viewing for anyone looking to watch the series, this episode an effective ghost story for a kids action/adventure show, with some of the most memorable scenes in the series.
4) Also from "Thundercats", you can watch "Spitting Image", where Mumm-Ra basically becomes Dr. Frankenstein. He has a lab in his pyramid (which we never saw before or after this and I have no clue where it came from) where he creates a clone of Panthro and gives it life by allowing it to be possessed by the evil spirit of the dead pirate Hammerhand. The stuff in Mumm-Ra's lab feels like classic horror material, and I love it, and some of the images of the Panthro clone causing chaos are more intense than you'd expect out of this show.
5) From "GI Joe", episode "The Phantom Brigade" works for Halloween. Cobra Commmander has had some screwball plans in his day, but few as nutty as this. Frustrated with his defeats at the hands of GI Joe, the good Commander hires a gypsy woman to raise the spirits of three dead warriors that he uses to fight his enemies. It is appropriately weird and perfectly fitting for this time of year.
6) From "Transformers" Generation 1, check out the post-movie episode "Dweller in the Depths". The creators of the Transformers, the Quinetessons, devise a plan to retake Cybertron. They trick Galvatron and the Decepticons into unleashing machine/organic hybrid monsters from Cybertron's core, including a giant energy leech. The leech is appropriately creepy as it can drainsthe energy of any Autobot and Decepticon it comes in contact with, turning all of them into energy vampire/zombies themselves.
7) From Duck Tales, any fan of Scrooge McDuck should check out "The Curse of Castle McDuck" as Scrooge and the kids return to his ancestral home, revealing the curse of his family's castle which involves a ghost hound that haunts the grounds. You get nice atmosphere, a good mystery, a ghost dog, and a look into Scrooge's family history. What's not to love?
8) Also from "Duck Tales", there is "The Ducky Horror Picture Show" where Scrooge unwittingly hosts a monster convention as Duck World versions of classic monsters like Dracula, Frankenstein, The Wolf Man, The Blob, and various others make their way to Duckburg. This was a love letter to the classic films of the 30s and 40s, and a fun ride for any fan of those monster icons.
9) From the original "Teenage Mutant Ninja Turtles", there is "Case of the Killer Pizzas" where Shredder puts eggs from Dimension X on three pizzas as booby traps for the Turtles. The eggs hatch into Xenomorph-esque creatures that give the Turtles, Shredder, and everyone else plenty of trouble. It is a fun caper episode for the show and one of its most memorable showcases for the series. Also, the monsters themselves are memorable.
10) Pretty much any episode of "The Real Ghostbusters" will fit. It is designed to be watched at Halloween time. My personal favorite episode though is "Citizen Ghost" as it is basically a better Ghostbusters 2 than Ghostbusters 2.
11) Also, pretty much any episode of "Inhumanoids" will fit here too. Not many people remember this show, but man, if you like monsters, then this is for you. D'Compose is basically Godzilla meets Evil Dead, and any episode featuring him is worth checking out. There is also the character of Dr. Mangler AKA Nightcrawler. His origin alone is nightmare fuel for children. There are also only 13 episodes, so it isn't a heavy lift to get through.