G1 had a bigger rogues gallery than Friendship is Magic, whose major villains were usually restricted to two-part premiers or finales, and a lot of them were darker than you'd expect of a TV cartoon in the 1980s:
This octopus isn't the most popular villain of the series but he is a cruel tyrant ruler of the underwater kingdom, and hopefully never gets free of the net he is imprisoned in at the end.
This goat is one of the more popular villains. He is a dictator and abuser who tries to banish the ponies to the Realm of Darkness, only to be banished there himself.
The longest running villain of the series, this witch is quite dark and malevolent, causing two separate attacks that could have had disatrous results and killed many. We never see what the Flutter Ponies do with her at the end, but I have a feeling they took her out for good to prevent a third apocalyptic plan.
This lava demon is close with Hydia. He is the epitiome of power-hungry villains, who in his quest for greater power unbalances the magic of Pony Land, which could have brought about the apocalypse. He tries to have the Princess Ponies thrown into the lava pit ("Jump or be pushed!" said one of his minions), threatens to melt Gnash the Ice Orc, and constantly abuses his henchman Sludge causing him to betray him for the ponies. During the final battle he makes it clear he intends to kill the Princess Ponies and Spike ("Surrender and I might let you live!"), but is himself killed by the Princess Ponies.
Was there ever any doubt? Though his initial plan seems nothing more than eternal night (being the origin of the phrase "Night that never ends"), he also intends to enslave Pony Land and painfully turns ponies into demonic dragons to pull his chariot (including Applejack). What earns him the top spot in this list is that he threatens to behead Spike, a baby dragon, for Scorpan's failures. On more than one occasion. He also violently backhands Scorpan, who would have fallen to his death if there wasn't a haystack below him. And quite fittingly, he is one of two villains to unambiguously die in this show.
Tirek is also so popular that he is the first G1 villain to be rebooted for G4. (Second being the Smooze, who isn't a villain in G4)