In fantasy, there is:
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Into The Abyss (Demons of Astlan) by J.L. Langland: The protagonist is transported to a fantasy world in the body of a demon, complete with horns and hooves. The first novel is quite fun and refreshing, especially the typical reaction of regular people to demons. The sequel wasn't as impressive in my opinion.
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Goblin Quest (Jig the Goblin) by Jim C. Hines: Typical D&D setting, but with various tropes of the genre turned on their heads. As the title implies, the main character is a goblin, a classic low level antagonist in a D&D adventure, except he's rather smart.
For something more Science-Fiction:
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Admiral Who? (Spineward Sectors) by Luke Sky Wachter: The protagonist is put in the role of Admiral of a fleet of spaceships, much to his surprise. His extreme paranoia (with good reason since his family is reputed to be bloodthirsty tyrants) quickly becomes a boon to his survival but also a good source of fun for the readers.
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Confessions of a D-List Supervillain by Jim Bernheimer: The adventures of a mad scientist type villain, think Dr. Octopus to get an idea, in a post-apocalypse setting where most of those damned heroes have been turned into zombies. Fun and good action scenes.
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How to Succeed in Evil by Patrick E. McLean: Another superhero fiction with a villain as protagonist. I haven't read it yet but it's on my plan-to-read list and seems to fit what you asked.
Also check some of the works of A. Lee Martinez, notably:
In the Company of Ogres,
Monster or
Emperor Mollusk versus The Sinister Brain. They all share the same irreverent, and parodic outlook on fantasy/SF fiction and often have traditional villains as protagonists.