I agree @Emperor Hydra I too am not too crazy that they take beloved childhood characters and turn them into gruesome horror flicks. Also, as far as those old horror flicks go, I prefer Frankenstein and Bride of Frankenstein myself, mostly because I've been a Franken fan since childhood.
Oh, yeah. Although I much prefer the original Dr. Doofenshmirtz, mostly because Alternate Doofenshmirtz as I like to call him tried to kill him along with Phineas and Ferb. That was not cool.
I'd say Demona from Disney's Gargoyles. I mean, there was that one episode where she traveled back in time and her past self met her future self.
I'd say Jimmy Crystal, mostly because he insulted Buster and his friends on TV by calling them no-talent losers, including my favorite character Ash. That does not score him very many points in my book.
Honestly, first time I saw the Star Wars crossover episode, I was expecting Doofenshmirtz to be named "Doof Vader."
Dr. Frankenstein (Alvin and the Chipmunks Meet Frankenstein)
Emperor Zurg (Toy Story 2)
Huxley (The Adventures of Elmo in Grouchland)
The Postman (Olive the Other Reindeer)
Snidely Whiplash (Dudley Do-Right [1999 movie])
Randall Boggs (Monsters, Inc.)
These are my favorite villains whom I know are arrested:
Aunt Spiker & Aunt Sponge (James and the Giant Peach)
Snidely Whiplash (Dudley Do-Right [1999 film])
Uncle Augustus (Here Come the Littles)
Vector (Despicable Me 4)
Shego (Kim Possible: A Sitch in Time)
Gloomius Maximus (Rolie Polie Olie: The Great Defender of Fun)
The Terribly Deep Thinkers (In Search of Santa)
Jackie Frost (Here Comes Peter Cottontail: The Movie)
Madame Gasket (Robots)
Oh, I forgot to mention...
Gallaxhar (Monsters vs. Aliens)
Dr. Facilier (The Princess and the Frog)
Boggis, Bunce, & Bean (Fantastic Mr. Fox)
His death is among my favorite Disney Villain deaths and/or defeats. Sure it's one of the most overused villain death tropes, and yet it never fails to be one of the best ways to snuff out a villain.
King Malbert (Igor)
Robert the Terrible (The Pirates Who Don't Do Anything)
Tai Lung (Kung Fu Panda)
Mr. O'Hare (Dr. Seuss' The Lorax)
Pitch Black (Rise of the Guardians)
Edgar E. Gore (Frankenweenie)
King Candy (Wreck-It Ralph)
I actually like both of them equally, so I can't really pick one over the other.
As a long time bear fan, easily Lotso.
Archibald Snatcher (The Boxtrolls)
Lord Business (The Lego Movie)
Bad Cop (The Lego Movie)