When I think of "villains" within the Olympian Gods, I always think of Hades. Most would say this is because he is the god of the underworld. However, in Greek religion, all souls travel to the underworld. So, associating Hades with the devil is not entirely accurate. However, there is something creepy about a god that spends all of his time with the dead souls beneath the ground.
Hades is weird for a number of reasons. First, he prefers to stay in the underworld. Therefore, when the other gods met on Mt. Olympus, his throne would be left vacant. When I was researching mythologies in high school, I actually found very few with him in them. So why classify him as a villain? It all comes down to one mythological tale.
Hades caught a glimpse of young Persephone as she was frolicking in the fields. His desire for her causes him to kidnap her and bring her into the underworld. Most of the Olympian Gods ignored the issue until her mother, Demeter, sent the entire world into a state of winter due to her anguish. The story goes that, because Persephone ate some pomegranates, she must split her time between Earth and the underworld.
This story presents certain "villain" character traits:
1. he is selfish and will maneuver for his own interest at the cost of others
2. he does not care about the feelings of other people
3. he is willing to take drastic measures to get what he wants
4. he excludes himself from the social norm (the sign of a psycho, I think...)
5. he prefers hanging out with dark characters (like a three-headed guard dog)
There it is. My defense of Hades as a villain. But, as all interesting villains, he does have his own goals, reasons and personality. He is a complex god, but most definitely also a villain.