I'm watching Empress Ki for the 2nd time, and the main villain is so great that it blows almost everybody else out of the water.
I'm talking about Jeon Gook Hwan in the role as Yeon Chul, the grand councilor. He's so scary, brutal and overwhelming that I can't think of any other villain character on the same level. He's my all time favorite villain, almost like the sidious emperor in Star Wars.
And also in Empress Ki is Baek Jin Hee as Tanashili (empress), a totally wicked character that is out of her mind, but at the same time a little pitiful character.
Another great character, in a sageuk drama, is Go Hyun Jung as Lady Mi Shil in Queen Seon Duk. In a way she's a similar character as Yeon Chul, just the female version really. I didn't find her as scary and brutal, but a villain for sure, and a little pitiful character.
Other noteworthy are:
Ok Taec Yeon as Jang Jun Woo in Vincenzo, a total sociopath.
Lee Jung Jin as Yi Rim | Lee Sung Jae in The King: Eternal Monarch , great villain but not like a insane guy or a sociopath, just a smart villain.
Yoon Je Moon as John Mayer / Kim Bong Goo in King2Hearts , a james bond level (Spectre) main villain.
Shin Sung Rok as Lee Hyuk (the emperor) in The Last Empress , a total psychopath with a nice guy facade and a totally wicked psyche.
Kim Mi Sook as Paek Seong Hee in Shining Inheritance , a totally wicked step-mother that makes you grind your teeth with her evil doings.