Graymalkin, Jill the Witch's familiar and accomplice of Snuff, from the novel A Night In The Lonesome October[?] by Roger Zelazny, (a graymalkin or grimalkin is an old or evil-looking she-cat)
The film Cats & Dogs[?] postulates an ongoing war dating back to ancient times between cats and dogs. The most notable cat is a spoilt Persian called Mr. Tinkles who is also an evil genius.
Blofeld's unnamed cat from the James Bond movies, which has inspired a number of imitations and spoofs (see Mr Bigglesworth, Madcat, and Nero)
Nero, a fluffy white caterpillar, pet of the villainous toad Silas Greenback, from the cartoon series Danger Mouse[?] -- a parody of Blofeld's cat (see above)
Schrödinger's cat, hapless victim (or lucky survivor) of a thought experiment by Erwin Schrödinger illustrating the incompleteness of the theory of quantum mechanics (although Schrödinger himself is historical, the cat is the protagonist in a thought experiment and thus fictional)