Alien Animals

There's an animal on this planet that's always looked harmless - rabbits or mice or puppies, it doesn't matter. One day, you'll be walking your puppy Mr. Flufferkins along and suddenly he'll look up at you and say, "Thank you, human, for this relaxing walk and all those times you've scratched my chin, but I'm afraid the Nogov 10th Brigade is coming here in five of your Earth minutes to get rid of this small blue planet and replace it with a transgalactic outlet mall. However, this is good news: you can spend your last five minutes secure in the knowledge that everyone will be getting cheaper outlets soon. Well, except the human race, of course, but these things have to be built. Goodbye." And then he disappears before your very eyes, along with every other puppy on the face of the Earth.

You've just encountered the Alien Animal. These aliens don't have green skin or rubber foreheads, they just look exactly like a specific type of animal. Maybe they make up the entire population of that animal on Earth or only part of them. Sometimes they're leaving Earth because they have knowledge about the impending end of the world and sometimes they just like watching television. Just relax and go with it.

Comic Books

 * In one Fantastic Four story Reed Richards hypnotized some alien shapeshifters called the Skrulls into thinking they were ordinary Earth cows. Years later those alien cows got mixed in with Earth cows and some were slaughtered for beef. The alien flesh though gave some people a virus that let them shapeshift their bodies into deadly weapons and detect hidden skrulls and it would also eventually kill them. The best part? There is no way of telling which cow is a Skrull until you eat it.

Film

 * The Cat from Outer Space. The lead cat arrives in a spaceship and falls for one of the native cats. Oh, and this is a live-action film otherwise starring humans.
 * In a nice nod to something not unlike realism, he depended on a jeweled collar for telepathically communicating with humans and telekinetic manipulation of objects.
 * Frank in Men in Black is by all outward appearances a regular pug. However, he is a fully sapient and sarcastic alien.
 * In the animated series, he is revealed to be...
 * Similarly averted in Zathura, where It's Not A Goat ... and it's not on Earth, either.

Folk Lore

 * There is an old British tale (there are different Scottish and English versions, probably some Irish too) about a man that comes across a funeral performed by cats on his way to home. The deceased is a cat in a crown holding a scepter (or the coffin is closed and the crown and scepter are painted over the coffin). When arriving home he tells the strange story to his wife, moment in which the house cat suddenly exclaims "The Old Tom/Tim/Pete/whatever is dead? Then I'm the King of the Cats!" and promptly runs out of the house.
 * The chupacabra. a hairless doglike animal that feeds on goats blood -- it was said to be a pet left behind by aliens.

Literature

 * The Hitchhiker's Guide to the Galaxy, where the above quote comes from. However, dolphins are never mentioned to be aliens, but rather just much, much smarter than humans. It's white mice who are the aliens, granted they're Human Aliens in their own plane of existence.
 * In the sequel, we learn that Humans are in fact aliens as well, descended from telephone-disinfectors and the like.
 * According to novels, it would seem that dolphins are the only native sapient life on Earth.
 * Also in Animorphs, domesticated dogs are the product of Pemalites bonding their souls with wolves before they became extinct. So that counts. Sort of.
 * Not an animal example, but one of the side stories indicates that broccoli was brought to Earth by aliens.
 * The cats in the book Star Ka'at and its sequels. Earth cats were colonists from a planet of sentient cats; when Earth got in danger, the advanced alien cats went to retrieve the Earth cats.
 * A Spider Robinson story in the Callahan series reveals that we find cockroaches distasteful because they are the degenerate descendants of an evil alien race of overlords.
 * In one Mandrake the Magician story, Narda has a dream (Or Was It a Dream??) about finding out that cats and dogs are two warring alien species; the ones on Earth were spaceshipwrecked here, and have exploited the dumb native humans (specifically, cats the females, dogs the males) to survive in comfort without their technology.
 * Cthulhu Mythos: The Cats of Earth's Dream Lands are notable for their intelligence, grace, ability to leap across the interstellar void and their ongoing war with the Cats of Saturn.
 * Cat-A-Lyst by Alan Dean Foster is another one where cats are really advanced and (mostly-)benevolent aliens.
 * There's a short story by Orson Scott Card in which dogs one day start speaking human languages and announcing that they're aliens -- and nobody takes them seriously; even when they start demonstrating their advanced intelligence by solving complicated math problems and the like, everybody shrugs it off as just a cute trick.

Live Action TV

 * In Doctor Who, it's the.
 * In "Survival," the Cheetah People's minions the Kitlings look exactly like Earth cats, except that they can teleport.

Newspaper Comics

 * In '80s Ziggy Sunday strips, the titular character's pet parrot turned out to be an advance scout for an alien invasion force. This idea since seems to have been dropped.
 * A Garfield cartoon suggests that cats are invaders attempting to subjugate humanity, and that they are responsible for certain seemingly-mindless actions of dogs and lower-class humans.

Video Games

 * Star Control 3 had the aliens as cows.
 * In the game Sheep you have to lead the sheep, who have become stupid in the time they were on Earth, back to their home planet.
 * Baldur's Gate: Boo, the miniature giant space hamster. At least if you take Minsc's word for it.
 * A regular space hamster (i.e. a hamster living on a spaceship) resembling Boo makes an appearance in Mass Effect 2.
 * Ordinary giant space hamsters does in fact exist in the setting (they were bred by a bunch of crazy gnomes to help power their spacefaring 'Jammers), as does miniaturisation magic, so a miniature giant space hamster could well exist. Unless Boo is an Awakened Miniature Giant Space Hamster, however, he should be just as intelligent as any hamster.
 * Some of the NPCs from Super Mario Galaxy appear to be either bunnies, penguins, bees, and orcas. Super Mario Galaxy 2 actually introduced NPCs such as hummingbirds and chimpanzees.
 * Can be created in Spore; you can make creatures that look rather like real animals...or you can make Starfish Aliens.

Western Animation

 * There's an episode of Invader Zim with warlike alien raiders who look exactly like babies.
 * In one Darkwing Duck episode ("Twin Beaks"), the hero gets help from aliens that look exactly like Earth cows -- though this is not exactly this trope, since it is probably only these cows that are aliens, not all cows on Earth.
 * Possibly a Shout-Out to the Fantastic Four story mentioned above, in which Reed hypnotized some shapeshifting aliens into mode locking themselves as cows.
 * In the animated series of Men in Black it is revealed that Frank the Pug looks very much like a dog anyway underneath his disguise suit.
 * Kat comes from a planet where everyone not only looks like cats, but their language is cat-like, and they have many of the same behavorial patterns as Earth cats. Oh, and there's a race of alien hamsters, too. They're everywhere!
 * On Teen Titans, an alien is visiting Earth when its intelligent pet, which looks like a green dog, escapes. Meanwhile Beast Boy, who can turn into a green version of any animal, is impersonating a dog. Hilarity Ensues.
 * The species of highly intelligent (and highly cuddly) cats from Futurama. They're here to enslave and kill humanity, natch.