Queen Chrysalis followed closely by Tirek and Sombra.

Think about if that cult bitch stolen your talents of who you are? She would leave you to die while! Starlight Glimmer ruled Equestria the dark ways of Witchcraft and magic .

He literally stole all the magic in Equestria-until the Mane Six acquired Rainbow Power and beat his ass.

Glimglim, Moony, Disco, Triskie, Sunny, and Glory have all been reformed, and Glimmy and Gloglo had legitimate, if misguided reasons for doing what they did. Chryssi may not have been reformed, and obviously went about things the wrong way, but at least she had a reason. And the Manes is insane so she can plead with that. Of the remaining villains, Sombrero seems like the worst to me.

Out of everybody else, he seems to be the strongest bad boy around, as long as he can keep all the energy he saps from all his victims. Every other (ex)villain is weak compared to him. Let's also remember that he is the destroyer of landscapes and has a burning hatred for little multicolored horses, compared to Scorpan, who loves them.

She could have ended all of Equestria

Queen Crystlis. She ponynapped the main 6 and the princesses and shinning armor in the season 6 final. The changings changed into nice changlings, but Queen Crytis still is mean! she took place for Princess Cadence for her wedding and put Shinning armor under a spell, or a trance.