NBC (ended 1969)
of The Original Series?
Garth in Whom Gods Destroy was great... "That's Lord Garth!"
Upon a little reflection, I find the humanoid opposition more formidable than the alien/monster selection throughout the series.
Since both Garth and Khan have already been chosen (and both are excellent choices), my choices (can't think of just one good one) are:
Trelene (who turned-out to be a spoiled energy-being child, maybe a Q, unconfirmed)
Mirror Spock (who turned-out not to be so villainous after all)
Klingon commander played by Baltar
Gary Mitchell (who didn't ask for what happened to him)
Klingon commander played by Mr. "I Dream Of Jeannie"'s husband
Harcourt Fenton "Harry" Mudd
Dr. Tristen Adams (one of two of Barney Miller's bosses)
Balok (also not so villainous in the end)
Romulan commander played by the late great Mark Lenard
"The Doomsday Machine"
Captain Ronald Tracey, and the
M-5 Computer (who committed computer suicide for it's actions)!!!
I always thought Claudius Marcus in Bread and Circuses was sinister.
The salt monster akaNancy in The Man Trap gave me the creeps as well.
Khan. Runner ups are characters with multiple appearances.