In action stories, often the story's quality is determined by the quality of the antagonist as much as the quality of the main characters. The antagonist acts and the main characters react, creating the drama that pulls at our heart strings and excites us. The more complex the story, the more likely the need for a strong antagonist will exist, at least in modern fiction. I decided to put down my top ten and my reasons for making them my top ten here. These are my top ten, but there isn't a particular order to them, save for the top five being the absolute best.
1- Shannon Wordsworth-
The main antagonist of Evolimit, a VN written by Higashide Yuuichirou. Shannon was a CIA agent, one of the project leaders of the Mars colonization project, and one of the most brilliant minds of his time. Scientist, spy, martial artist, leader, pioneer... these all describe parts of who he is, but the heart of who he was was someone who desired more than anything to see how far he could go, how far he could take himself. The discovery of Marscyte, a mineral on Mars that, when implanted into the human body, allowed for self-evolution and the attainment of unique abilities, was the element that sent him off the deep end. His desire to see how far he could go was transferred into a desire to see how far he could evolve, where the end of his potential could be. This resulted in the events of Evolimit's story and the conflict between the Disasters and the residents of Mars. Unlike many villains, he is neither insane nor devoid of feelings toward those killed or harmed by his actions. He is pained by the act of turning his friends into Disasters, and it agonizes him that he is using his protégé, Shiranui, to aid in his rise. However, his emotional pain in no way convinces him to set aside his goals. The fact that there is nothing particularly twisted about him beyond that desire makes him one of the more striking and impactful antagonists I've ever seen.
Dies Irae's true antagonist. A god who desires his own death at the hands of the woman he fell for, Marie. He is perhaps the most inhuman in personality on this list, because of his hundreds of thousands of years of subjective experience. It says everything that he 'replayed' all the horrors of Earth's history innumerable times solely to get his ideal result, warping entire generations in subtle ways and twisting the souls of men and women beyond hope. Is he evil? Undoubtedly. Is he a great antagonist? Indubitably.
3- Kefka- Final Fantasy VI's main antagonist. He is frequently listed as one of the craziest bad guys in all of gaming history, with good reason. He is the nihilistic result of experiments with granting humans magic, and as a result he gets the bright idea to destroy the world... and actually succeeds. His psychotic laughter (in 16 bit sound) is familiar to anyone who played the game, and his psycho clown character traumatized an entire generation of gamers into thinking clowns are inherently evil.
4- Christopher Valzeride- The heroic antagonist of Silverio Vendetta.
When I say heroic, I mean it just as that. Valzeride is a true hero and patriot of his nation, Adler. Beginning as a child in the kind of slums that would make most third-world nations turn up their nose in disgust, he rose up through Adler's military based purely on his own merits. A man of only average talent, his iron will and willingness to push his body and spirit beyond their limits on a daily basis transformed him into an unstoppable force within Adler. He became the first survivor of the initial Esperanto body-modification experiments, and, after the blue-blooded aristocrats lost their political fight with him, became the first non-aristo Fuhrer of Adler. His example became the thing every young man wanted to be, and he could inspire even the most mean-souled with a few words. Ironically, Valzeride's greatest flaw is also the thing that allowed him to rise so high... his absolute commitment and inability to give up. To him, acting for the greater good and driving himself beyond his limits are the default. He honestly couldn't do anything else if he tried, and he is aware that his true nature is 'the enemy of evil' rather than an 'ally of good'. In fact, it is his own actions to protect the country that instigate the events of Silverio Vendetta and lead to his own end.
5- Reinhardt Lohengrin- Legend of the Galactic Heroes- While he can also be considered the protagonist of the massive space opera, he is also an ongoing antagonist. Reinhardt is an ambitious young man whose meteoric rise in the militaristic and expansionistic Galactic Empire are driven by his twin desires to wrench his sister away from her position as the incompetent emperor's mistress and conquer the galaxy. A fierce man with a warrior's demeanor that usually only serves to fuel his strategic and tactical victories, he honors both enemies and allies who show ability and contempt for those who rise above their level of competency. As a ruler, he is ruthlessly fair with those of ability who are capable of loyalty and brutally ruthless with those who are incapable of it. As an enemy, he is one of the most frightening (non-magical) men in any anime, game, or VN I've ever seen.
Lilith- Say what you'd like about Tokyo Babel, but having one of the heroines as an antagonist actually worked out pretty well here. Lilith, for better or worse, is a demon. She is a very demon-like demon with the twisted and often contradictory desires that accompany that, especially after she becomes an antagonist. As one of Lilith's many 'illusions', she was a cheery and mischievous woman who often indulged in sloth and generally whimsical behavior. After becoming the true Lilith and fusing with Tiamat, she is fused with Tiamat's desire to be the goddess of all creation while being free from mortals. It's hard to say which version is worse, though, lol.
7- Mikado Ruri-
As Hello, Lady's true antagonist, only revealed in Saku's and the true path (existing in the Superior version), she is probably one of the freakiest lolis I've ever seen. Her unique ability 'Overcome' (an inherent ability that allows her to overcome any type of harm or stimuli that she has experienced before to the point that it no longer effects her) and her complete lack of empathy make her a horrifically frightening opponent. One of the few truly evil characters (as in, iredeemably so) on this list. Ruri is a girl who, when she discovered a plot to massacre her family, asked her childhood friend not to reveal it to the family beforehand, solely so she would have a chance to be free from the chains her family sought to put on her.
8- Reinhardt Heydrich- Well duh, we all knew he would be on this list. The anime-ified version of the infamous SS officer assassinated in the middle of World War II, he spent most of his mortal life as an utterly competent individual who rarely showed any real emotions. It was only after his encounter with Mercurius that his true nature, as a monster of mythical proportions, began to shine through. His true nature was that he loved all things but that his desire to destroy them was inherent in that love. With Mercurius's intervention, he became intent on creating a world where all were immortal, that he could break those he loved continuously while never actually losing them.
Victor Goodman- One of the antagonists of the Baldr Sky Zero duology. A man with two personas in a single body, one the commander of Squall, the other the pilot of the Simulcram that killed his wife and used her clones continuously as weapons. As the leader of Squall, he was a gleefully murderous commander who always had his men's backs and delighted in wreaking havok on the battlefield and making a profit at the same time. As the pilot, he was a cold-blooded man who existed solely to fulfill a role given to him long ago.
Gilbert- The plotter that manipulates everything behind the scenes in Silverio Trinity. A follower of Valzeride, obsessed with his personal ideals and willing to do anything to see the return of the Light lost when Valzeride fell. Like many followers of the Light in the Silverio series, he is willing to do horrific things in the name of his cause, all the while promising that their sacrifices will be made good in the future he creates. He loves those who struggle, who work to rise above the suffering and tribulations life throws at them, and he is utterly contemptuous of those who don't. He believes firmly that the victor should always receive the spoils, and he hates it when that isn't the case.