May I point you in the direction of Dolores Umbridge?

Voldemort was the main bad guy in the entire series, yet there was still parts of me that appreciated him. His way of thinking was not his fault. He was conceived by a love potion, so he could not feel love. He was orphaned and teased, and he rose above all that to build his ideal world of cruelty. He hated muggles because his father was one. Because muggle children rejected him.
Then there's Umbridge. 
You hated her outright and without doubt. She was mean. I feel much more cruel than Voldemort. And she did it with a pink lipped smile and a giggle. She is probably the best example of a villain I can think of right away. 

There are so many different types of villains. 
There are ones who believe adamantly that they're doing the right thing.
Ones who simply want to mess things up. 
Ones who are after power.
Or Revenge.
Each villain depends on the story they're in. 

In my longest running rp, I've had villains who are the source of all things terrible simply because its their nature. 
I've had an enemy who feels he's doing the right thing and taking whats due.
There was a young man who was quite sweet, but nearly killed a mess of people because the woman he loved was at risk.

Each villain is different. 
I think what makes them is simply their actions. Could be action that range from total death and destruction to just marring the peace.