Okay, my 2 cents....
1.) King Sombra: He is without a doubt, hands down the villian of choice. Not only was his appearance and voice freaky but he wasn't just after the Crystal empire. As Princess Celestia said, if love and harmony radiate from the empire, those things radiate all over equestria. If hatred and darkness rule....It would be my guess those things would envelop equestria instead. That ability to see the big picture adds to his fearsomeness. Further, his magick is plain evil. Spells to make you realize your worst nightmares? Keeping an entire kingdom as slaves? This guy was certainly no joke.
2.) Queen Crys: Its hard to know where to start with her. She did so much to hurt so many. She disgraced Twilight Sparkle, nearly managed the fall of canterlot, took Princess Candence's place and threw the real pony in a dark hole under the city. The real princess looked horrible when she was found. She brainwashed 4 different ponies and of course didn't only use Shining Armor to feed of his love but wanted him as hers for really no other reason then because she could. "No I do not love the groom, in my heart there is no room". Feeding off of the energy of love is one thing but to steal another love from somepony just because you can is pretty dark.
3.) Discord: Not a very scary villian to me. Yes he was highly intelligent and clever, yes he managed to defeat the Mane six, but his end goal was chaos. Up is down left is right, chocolate rain, no gravity....all these things are pretty annoying but not evil. What he did to the mane six he did so they couldn't use their powers, but he didn't really harm anyone. I was amusing and I liked the character but outside of that he didn't really have me shaking.
4.) Nightmare Moon: Misunderstood. Her plan had always been to cover the world in endless night, not to make the ponies suffer but because she was jealous of everypony sleeping through her beautiful nights. She wanted to be loved and since she couldn't have that she would at least make them have to live, work, play etc at night. I felt more sorry for her then anything else. Yes she does have some pretty dark magick, but thats not the same as Sombra's Black Magick.
I think thats all I got. Cheers!
Obsidian Winter