A thoughtfully created antagonist plays a huge role in making any story memorable. Some of the most revered antagonists are those who are good guys at heart. They are often misinterpreted, misunderstood, wrongly persecuted or driven to their current state simply because they were in the wrong place at the wrong time.
The Monster of Frankenstein
Among the most iconic works of horror literature is Mary Shelley's Frankenstein (which has ABSOLUTELY NOTHING to do with the upcoming “I, Frankenstein” movie in case you were wondering; those of you who didn't read the book please don't let that movie ruin it for you). The book was about a scientist who wanted to play God and ended up being chased a long way by his own creation, a terrifying monster on a killing spree. What makes the monster such an iconic villain is how right he is to feel his 'birth' (which was a rather boyish experiment) to be unjustified. His hatred towards a creator who created him imperfectly and thus causing him to be unacceptable to the world (I'm quite sure a lot of us felt that at some point in our lives). His rage drives him into being the iconic frightful monster that has endured the test of time and still gets appearances in horror movies and media.
Roy Batty (Blade Runner)
From director Ridley Scott's 1982 flick, the very charismatic Roy Batty is a Replicant, a created human being with a four year life span and artificial memory. In the movie he is hunted by the Blade Runner, Decker (Harrison Ford), who does so as ordered to protect the corporation creating replicants. The whole movie is about the ethical side of using technology, of creating tailored life forms for the convenience of certain stakeholders. The main underlying theme is choice. Throughout the movie Roy Batty looks for a way to increase his very brief life span which leads him to his ruthless criminality. In a sense he is the protagonist and a rather tragic one being hunted by the authority of which he himself is a creation and a victim.
The Big Boss, Liquid Snake And Solidus Snake (and pretty much any major Metal Gear Solid Villain)
The Metal Gear series is convoluted and dramatic in terms of storyline and characterisation. Each and every villain is complex and charismatic. The Big Boss (aka Naked Snake) who also happens to be the other protagonist of the MGS Chronology aside from Solid Snake (and an antagonist in the beginning of the franchise) is the founder of Outer Heaven, a nation of free soldiers. Soldiers who are not bound to a nation and are not pawns to shady motives of powerful people create a nation of soldiers who wished to fight, but not for a politician. It was in his eyes a true, free world for soldiers. This was considered “evil” in terms of the perspective of America, because by doing this, Big Boss became the defector and the opposition and most importantly a force to be reckoned with. Snake, the hero of the series was sent to kill him (in the very first 2D Metal gear game), but again only because he was told it was what he had to do by the American Government. Once again, a major theme behind the whole story is choice, and the darker side of running the world's biggest democracy. The Big Boss, as well as his successors the Liquid Snake and Solidus Snake fight for an ideal world where there are no borders and no soldiers just following orders for purposes any other than their own. Their vision is one of a world where people “will be able to see that we are all just inhabitants of a little celestial body called Earth. A world without communism and capitalism.” The whole story is about how the ideologies of different characters conflict, leading to the events in the saga birthing the misunderstood and prosecuted villains.
It is interesting how often villains are easier to relate to than some protagonists. What any writer can do with a villain adds a million dimensions and possibilities to shaping a story.