My favorite/best villians . . .
5 - Doomsday Machine/Nomad/M5/Gorn
4 - Henoch/Losira/T'Pring/Trelane/Balok
3 - Romulan Commander(BOT)/Romulan Commander(TEI)/Kor/Lenore Karidian
2 - Mirror Spock/Evil Kirk
1 - Khan
As for the other part, I don't care for 'worst of' anything lists regarding Star Trek
Ah, you're cheating!
But seriously, I feel you on this. I should clarify that when I talk about "the worst of anything" to do with TOS, keep in mind that I am discussing it within the context of TOS which, because I consider it to be the most awesome show in TV history, any of its "worst of's are absolutely stellar compared to what can be found in any other program.