A Bug's Life: Molt is very cheerful and friendly, unlike the rest of the grasshoppers. He never really does anything bad in the film, and ultimately makes a Heel-Face Turn.
An American Tail: Fievel Goes West: Cat R. Waul is a cultured, well mannered "gentlecat" who lures New York mice out west in order to turn them all into "mouseburgers", because simply chasing and eating them is an "unnecessary expenditure of calories".
Gru is gradually softened into this over the course of the story.
El Macho from the sequel counts too. It's pretty clear he's incredibly nice, even after he's revealed himself to be Not Quite Dead.
Frozen: Duke Weselton is this. He will kill to have his way (to secure trade advantages) but shows care and concern for his soldiers as well as the people of Arendelle.
The Jungle Book: Kaa, despite wanting to eat Mowgli, comes off as very polite and soft-spoken.
Lilo & Stitch: Jumba Jookiba may constantly boast over his status as an evil genius, and he may have created over 600 super-destructive aliens, but he's a pretty decent and sociable guy overall. He even gets a Heel-Face Turn near the end of the movie.
Monsters, Inc.: Waternoose is genuinely friendly with Sully, and is sincerely regretful when his plans require trapping him in the human world. He even tells off one of his Mooks for not being half the monster Sully is.
The Sword in the Stone: Madam Mim is cheerful, amiable, and actually pretty friendly when Arthur blunders into her house, and while he can tell she's unpleasant, he doesn't even realize she's dangerous until she tells him she has to kill him which she says with about as much fanfare as someone saying it's suddenly started raining. Thought she's more a mix of this and Faux Affably Evil, sometimes her true nature slips out to show just how crazy she really is before she pulls herself together.
Stinky Pete from Toy Story 2. He's a folksy, almost grandfatherly fellow who legitimately believes he has Woody's best interests at heart. However, it can't be ignored that he forces his beliefs onto other toys and manipulates them to his own ends.