Well a good place to start would be from the likes of Koba from the reboot planet of the apes movies or Lotso from Toy Story 3 since those two were given some background as to why they do the things they do.

My advice is to give that villain story and motive, so they'll start as an actual character that you might take into consideration.

A viable option is not having them START OUT as Pure Evil, but slowly fall down the Moral Event Horizon until they cross that point. Regardless if they are PE, maybe give them something you can at least relate to; like an actual hobby (outside of torturing and killing). For example; DIO likes reading.

Even if they are Pure Evil, you can find quirky ways to make them interesting and well-written such as Slade from the original Teen Titans. And even funny like Hades from Kid Icarus: Uprising.

Either that or well, really give them character. Give them their own likes and dislikes like anybody else... Aside from a simple pure evil, make them complex and interesting by giving them more perspectives other than just a senseless evil.

Jenna Zan Arbor from Star Wars is a good example. At the start of her scientific career she wanted to help other people. She deviced a vaccine that saved millions of lives. She also saved an entire planet from famine. However, after that she started feeling unappreciated because she didn`t receive enough money and fame. She also felt unappreciated by the Government because they refused to fund her projects. As a result she started spreading diseases on different planets so that she could later cure them and receive money and fame.

Personal insecurities, character traits and humanization that does not diminish how despicable they actually are, and maybe a tragedy that is quickly swept away because of how evil they are, or a delusion that they are correct somehow.

See: The Plutonian and Isaac Westcott.

Isaac can have an affable conversation with his employees, does have a sense of friendship and can be funny at times, like a normal human being, but then you realize throughout the story what his sense of honor and friendship are like, and it is incredibly twisted and he is extremely self-serving in his relationships.

The Plutonian was alone and unloved for most of his life, and was an outcast for most of his life until he became a superhero.

Even then, because of this extreme necessity of being loved and inability to take any criticism and relate to other people around him, he snapped and decided to kill everyone on the planet.