Dusknoir hid behind a mask of a simple explorer, trying to hunt down his prey. He made them all believe that he was the good guy and Grovyle was the bad guy, until he basically broke down the player and his partner's dreams by revealing himself to being the kind of person he is. He brings you up to basically worship him, and then knocks you down without reason. That is why he is at Number 5.
The Master is the kind of guy who you know is evil, and despite your knowledge that he is evil, you don't know what he will do next or how he will do it. As a child, he was basically corrupted by the time vortex, which drove him mad, into delusions of ruling the universe. Even when he lost control of planet earth, and was shot by his wife, he still managed to win in his own way and break the Doctor's heart by not regenerating, killing himself, and leaving the Doctor all on his own. He's at Number 4.
Smaug the Dragon is originally one of Sauron's top commanders, from what I've heard, and despite his role in Sauron's hierarchy, he basically betrays him, and goes off on his own. He manages to capture his own mountain and steal all the treasure for himself, but not before killing anyone in his path. So not only does he betray the good people, but he also betrays the bad people. You could say he's an anti-hero, but to betray your commanding officer takes a pretty good level of evil. Plus he's a big scary dragon. That is why he is at Number 3.
Loki was adopted into Odin's family by Odin himself. Being raised up to believe that he would someday amount to the power of both his brother and his father, his dreams of conquest were soon utterly shattered when he learned of his true heritage, and why Odin would never consider him as his own son, how he would never be able to stand a Frost Giant on the throne. Angered by this, he leads an invasion into Asgard, betrays the invaders, levels a small town in the south of the states, almost destroys New York, all the while doing a deal with the Devil. He is pretty evil, evil with a reason. This puts him at Number 2.
Enter Bane, the masked and dangerous criminal mastermind of the takeover of Gotham City. His dark history stems from him being rejected by the League of Shadows. Despite this, his strong but demented mind forces him to carry on Ra's Al Ghul's dreams of order in Gotham, but with more fire. Before he destroys the city, however, he wants to see the people's of Gotham's souls shatter into a tiny million pieces before the atom bomb goes off. On top of that, Bane locks Bruce Wayne into a jail cell with no possible way out other than a seemingly impossible climb, and a television set streaming live from Gotham. He creates corrupt courtrooms that bring in the most powerful people in Gotham, and murders them in cold water. A calculating mind inside the body of a beast is not something to be trifled with. Bane is at number 1.
Khan is a super human with an even darker past. He was put into cryo sleep 300 years before his reawakening, and was awoken to Alexander Marcus a man with dreams of a technologically advanced future in weaponry, and the Fleet Admiral of the Starfleet. In his own words, he was put to work on these weapons because he is simply "better at everything". Along with the rest of his crew, he was threatened by Admiral Marcus into building this mass weapon, or his crew would be killed. Outraged, Khan hides the bodies of his crew into the 72 torpedo tubes before escaping. He would then go on to bribe a father of his sick daughter into destroying a weapons hanger, stealing a ship to primarily open fire into a meeting of the Admiral and other high ranking officers, and ultimately poisoning Kirk's mind into taking out Admiral Marcus and stealing his ship. Khan then threatens Kirk and his crew by handing over his crew in the torpedoes before he destroys the ship. However, Spock ultimately decides to transport the torpedoes and detonate them on his ship (but not before removing the bodies of the crew), forcing Khan into a state of shock, madness, and anger, where he flies the ship into the center of San Francisco in an attempt to destroy Starfleet Headquarters, killing hundreds of people. Khan is ruthless, powerful, dangerous, calculating, and simply evil. He managed to take down a whole fleet of Klingons wielding nothing but one rifle. He betrays everyone he comes across, and makes you trust him before shattering whatever hope you have in him into thousands of tiny pieces. In effect, he is all of the aforementioned villains' best bits morphed into one. His sheer evil is beyond evil. That is why he deserves a place at Number 0 on my list.