To a lesser extent, Grogar and Surprise alongside the Friendship Is Magic crowd. The former was made into a real character in season 9, even if he didn't appear in the flesh, while the latter has a similarly-colored pony among the Wonderbolts.
There's also a surprising amount of fanart of the three witches. Them being voiced by popular (at the time) actors in the movie may help matters.
Genius Bonus: In "The Great Rainbow Caper", Danny and Surprise get kidnapped by the Gizmonks, and proceed to destroy their lab from the inside. When they escape from it, they do so by getting inside a giant wooden horse. Sounds familiar?
A more subtle example from 'Mish Mash Melee' where small, pastel-coloured 'droplet' creatures known as the Frazzits are scrambling the minds of the dell dwellers (and the episode's main ponies Wind Whistler, Fizzy, Gusty and Shady). Fizzy receives Wind Whistler's intellect due to the effects of the Frazzits' scrambling, while Wind Whistler becomes as much of a goofball as Fizzy normally is. While Fizzy is ordering Wind Whistler to take action, she refers to the Frazzits as 'protoplastic'. A 'protoplastic organisms' (the literal words used by Fizzy) is a plant, fungal, bacterial or archaeon cell which has lost its cell wall. The cell wall keeps cells rigid and prevents them from falling apart. As the Frazzits transform people's minds into their opposites, guess how the Frazzits affect the dell dwellers? They transform them from diligent workers into goofball with no sense of responsibility - they are no longer 'rigid' and their community is falling apart due to the Frazzits.
Growing the Beard: Many fans view the first four serials as of debatable quality. The show, however, finds its footing at "The Return of Tambelon".
Harsher in Hindsight: The episode "Bright Lights" features a pop star who is an homage to Michael Jackson, and his manager steals fillies' shadows as Applied Phlebotinum. Several years after the episode was produced, Michael Jackson himself began to face accusations of taking indecent liberties with children.
The Raptorians cross it by convincing Porcina to turn Ponyland to glass with everyone in it for their own selfish reasons.
Lavan is told that his plans for the Princess Ponies' wands might destroy all of Ponyland by throwing things into utter chaos (which is exactly what happens). He doesn't give a darn and goes ahead with his plans anyway, putting everything in danger out of his own greed. If that's not the point where he crossed the line, it's most likely when he tried to kill the Princess Ponies and their group by having them thrown into lava, primarily for spite.
Narm Charm: The cartoon's shoddy animation, amusing goofs, some silly voices, and occasional broken aesops all make the show a hilarious watch. But the setting, creepy villains, and some downright badass moments courtesy of the ponies makes the show awesome when it isn't silly.
One-Scene Wonder: In Mish Mash Melee, we get a personality-swapped Wind Whistler and Fizzy for a few glorious minutes.
Periphery Demographic: It's not uncommon especially after Friendship is Magic caught on to hear of male fans of this show. For many boys in the 80s and 90s, this was their first fantasy adventure cartoon.
The Scrappy: With exceptions, most fans loathe Molly and Danny. Shady can also fall into this.
Shocking Swerve: Some have criticized Porcinas HeelFace Turn for being completely out of the blue. Her reason is that she cant bring herself to turn the remaining ponies into glass because theyre alive despite the fact that she literally did just that in the previous episode.
Wangst: If you didn't feel that Shady's insecurities were warranted, then you saw her this way.
What an Idiot!: Good Lord, there are so many times in this series where the ponies or even Megan and her siblings do something stupid.