Clem he was definitely the most evil monster in the series.
In all seriousness I'd say the top 10 scariest monsters were as follows.
10/ Turok Han
Great concept, fabulous make up, effective performance from Camden Toy. The first Uber Vamp helped restore menace to Vampires who had taken a serious nerfing in S5 and 6. However their performance in the finale was a bit too underwhelming.
9/ Ken
Anne is underrated. Ken serves as a great metaphor for how people at the bottom of a society are chewed up and spat out and nobody cares. I also liked his death. It's one of Buffy's best heroic moments beating up his goons.
8/ Der Kindestod
One of the most terrifying ideas in the series, the death of Cecilia is nightmarish, and his look was scary. He had less personality than some other monsters however.
7/ Catherine Madison
Not sure if she's a monster, but what the hell I'll list her. A great metaphor for people trying to relive their glory days and force their children to relive their lives. She was menacing and her ultimate fate is gruesome.
6/ James Stanley and Grace Newman
One of the all time best episodes. Both the horror and the real life elements are disturbing.
5/ Glory
The most threatening villain, I loved the way she was kind of a dark reverse of Buffy. Buffy is the litte blonde girl who goes into an alleyway and gets ripped apart by monsters turning round and beating it up. Glory meanwhile is the little blonde who turns out to be the most ferocious monster of them all. I liked her backstory, her endgame and her crazy persona. (Apparently she was based on the Joker and I can see it on a recent rewatch. Her speech about her being the only one to see how crazy the world was, sounds like it could be from the Killing Joke.)
4/ The Master
My favourite Vampire king. Mark Metcalf's gloriously hammy performance, the make up, the concept and the fact that he not only killed Buffy, but arguably brought her to the limit of her terror more than any other villain (save Glory) I think earns him a spot on most fans lists. He was also in some of the best episodes in the shows history. The opening two parter, Angel, Prophecy Girl, The Wish etc.
3/ The Gentlemen
Do I need to say why? Such an imaginative, and nightmarish idea. The Gentlemen are an example of when everything comes together so perfectly. The make up, the way they glide, the paranoia of they can hurt you, but you can't scream. They are the big monsters of my generation.
2/ The Gnarl
Another one of Camden Toy's best performances. The Gnarl is the most frightening monster in possibly anything. The way it kills its victims, coupled with the grotesque make up and Camden Toy's gleefully evil, child like performance ensure that he sticks in your mind afterwards.
1/ Angelus
You can't beat Angelus. The most needlessly cruel, sadistic monster in the shows history. The other villains are merely willing to use evil to get ahead. The Master is willing to use evil to rule the world, Glory to get home, Warren to gain power for himself, Adam to create his new and perfect race, even the Gnarl just wants to feed. With Angelus however he does evil for evils sake, like when he lays Jenny's corpse in Giles bed and we see him smiling at Buffy and Willow crying over her death.
S2 is still probably the peak of the show for me.
Honorary mentions to the Mayor (one of the best villains for sure, but he wasn't a monster technically until the last episode.) Faith (for similar reasons) Spike who though a brilliant villain became more than just a villain and so really belongs in a different category.
