On Bolt, the villain of the Show Within a Show has two cats. The actors who play them love to torment Bolt (who thinks the show is real) by going to his trailer and make threats in character. After Bolt is lost, he mistakes stray alley cat Mittens for one of the Right-Hand Cats and tries to get her to take him back.
Inverted in Cats & Dogs where the villains of the film are cats who just happen to be led by a white Persian. The leader Persian Cat invokes this trope to interact with humans, using a comatose man in a wheelchair. The human's mouth has a bandana or something around it, so the cat make others think the human is talking, so as not to freak everybody out with a talking cat.
Subverted in The Powerpuff Girls. The girls once defeated an archetypal faceless villain who stole a valuable jewel to power a laser, and took his pet cat home afterwards. The cat was actually the villain all along and hypnotized The Professor into almost finishing the mass brainwashing project
•In Despicable Me, Gru has a bizarre-looking mongrel dog named Kyle. Hilariously, a bio-scan in the sequel is unable to even recognize Kyle as a dog. (SPECIES: UNKNOWN)
Early on in Megamind, the title villain uses one of his Brain-bots for this purpose.
In Revenge of Kitty Galore, the sequel to Cats & Dogs, villainess Kitty Galore (who's herself a cat, of course) has a white mouse as right-hand pet, whom she calls Scrumptious. The poor thing is treated pretty much as a Chew Toy and is in a state of near panic for the whole movie.
A mad scientist on Courage the Cowardly Dog had a right-hand rat named Rat. Rat mostly carried out errands for his manic-depressive master, but would also allow himself to be held and stroked if the morose scientist needed comforting.