Older Than Steam: Hamlet, speaking of his uncle Claudius who murdered his father, laments that "one may smile, and smile, and be a villain."
Abby and Martha Brewster in Arsenic and Old Lace are the kindest pair of old maid sisters one could ever meet. Better watch out, though, whenever they pour someone a glass of wine. Arguably, it's more an act of misguided charity than actual evil in their case.
The Wizard from Wicked is friendly, kind, and supportive to Elphaba, presenting himself as a kind father figure who only wants to help every citizen of Oz to fly. Unless you're one of the talking animals, in which case you are to be cowed into submission, brainwashed, and/or exterminated. Elphaba is his mirror image, nasty, insulting, and condescending to others, and flies into classic villain hissy fits (in the book, she mutilates an old woman's corpse because the woman had the audacity to die before Elphaba could kill her; in the play, she responds to her friend's death by having her minions unleash a wave of off screen terror upon Oz), but has good intentions. It's no surprise that the casual observer in Oz mistakes which one is the villain.
Smee from Peter Pan. He's not a nice man—after all, he is trying to kill the Lost Boys—but he's so unintentionally pleasant and charming in his dim-witted way that everyone loves him. Captain Hook observes that Smee is happy because he thinks that the boys fear him, even though he lets Michael try on his spectacles.