It is probably helpful not to think of antagonists as antagonists but rather as people with honest motivations (even if they are dark they can be honest) and a sense of purpose. When we truly understand a hideous enemy then we can feel that sense of intellectual disgust at their quest.
A good thing to give an antagonistic character is an anti-social hunger and a sociopathic ambivalence about fulfilling it. If the enemy is an addict, a sadist or a cannibal it instantly helps to mark them as the other. It is vital that their unnatural hunger should not make them weak except in the fulfilling of it. The rest of the time they should appear unassailable. A drunkard is not sinister unless he is only ever a drunken brute in the presence of those who are weak in comparison.
The antagonist should have some lofty goal, admirable philosophy or natural charisma. There is nothing to provoke rejection more than a good thing perverted. In these instances the antagonist has "heroic" qualities not "sympathetic" ones. Heroes in the classical mode are untouchable so this helps to reinforce the untouchability mentioned in my previous point. The other thing about these qualities is that they are easily perceived as double-edged. Those with lofty goals and admirable philosophies are prey to hubris, those with a natural charisma are open to the corrupt use of their natural likeability.
If the antagonist is organising a campaign against the hero it must be an understandable vendetta. The more the antagonist views the protagonist as an equal the harder terror becomes. Therefore, as already explained, the antagonist must be presented in such a way that they seem superior to the protagonist in terms of raw power on any suitable fronts: money, political sway etc. The problem is then the question of why the antagonist is acting against the protagonist. If the audience do not believe the antagonist has legitimate reason to specifically be targetting the protagonist then they cease to be a threat and become, rather, a complication, or worse, they just seem unrealistic. Whatever is happening, it must be personal, and the antagonist must have every appearance of winning.
The implied fate of the protagonist must be made clear. Meditate particularly on the possibilities of a "fate worse than death". If it is not made plain what will happen to the protagonist while they act in defiance of the antagonist then people won't feel the tension. Threats to heroes in writing are most often to do with attacking that character's identity. If you threaten to break a PI's fingers that's a complication for the PI, his fingers will work again at some point to the required level. If you threaten to break a surgeon's fingers that could be the end of his career, a clear threat to the surgeon's livelihood and identity (it must be plain that the surgeon enjoys her work). Threatening a protagonist's loved ones is always a low trick that proves effective.
Marrying evidence of intellect to evidence of brutality is always a winner. Look at the archetypal Batman foe, The Joker. The coupling of a quick wit and a sadistic temperament make it seem, to get Freudian for a second, that the id and the super-ego are united in attacking the ego in a pincer movement. Antagonists that combine possible genius with ugly bestial urges are always the most theatrical of the species. Going to extremes, however, can always help us to later approach the same matter with subtlety.
Fear must be accessible. Trying to manufacture a scare from a complex image, such as a statue of a kangaroo with a red ribbon tied around it is doomed to failure. However, simplistic cues such as an eyeless doll with a crack in the skull, are easy for an audience to visualise and therefore more likely to have an impact.
With that last point it is always important to use such cheap tricks sparingly. It is mainly the ugliness of the perverted appetite coupled with the dangerous beauty of raw power that will push the buttons most readily.