Paranormal Activity 2
A dog is attacked, pulled off screen and knocked unconscious. She is taken to the vet and we don't see her again.
A dog being walked appears very briefly in one scene. Nothing happens to it. In another scene, a rat jumps out at someone and then disappears.
Only animals in the film are some CG birds that are never put into harm's way.
Two mules are shot. Their bodies are seen and thrown off a bridge and into a river.
A dog is apparently crushed (off camera) by a spaceship. Later, an alien eats a live bird.
A dog is shot but it survives.
Penguins of Madagascar
Animated. None of the main characters die, but a bird that lands on a ghost ship is gobbled up by a ferocious seal while the main characters watch.
There is a sequence where Mima comes home to see that her pet fish have all died while she was away, at which she has a nervous breakdown. It later becomes a plot point when she realizes that she's in a replica of her home, based off the fact the fish are still alive.
Two dogs, Achilles and Apollo, are shot in the head and killed.
The main character works at an animal shelter where his favorite dog is put down.
Pet Sematary II
Where to begin? A pet dog is shot, dies, comes back to life evil and after a lot of mayhem, it is killed again. An elderly dog is euthanized. Rabbits are graphically killed by a man. A kitten is threatened by bullies. More kittens are mauled.
Phantasm IV: Oblivion
A dog is run over by a villain. There is a close up on the villain when the dog is run over so we only hear it happen. This scene appears in the Extended Cut DVD edition of the film.
A dog is killed when a monster rips it apart from the inside.
A horse belonging to a main character is tormented and trapped by killer ants, leading to a man having to shoot and kill it. An adorable mouse in a research center is devoured by the ants.
A rabbit is run over by a car offscreen.
Planes, Trains & Automobiles
After riding in the back of an open bed pickup truck in freezing temperatures, two men and the aggressive dog riding with them appear comically frozen for a few moments.
A dog dies in a horrific and bloody way. Great movie, one horrible scene.
During a chase scene a large dog is thrown at a man as a distraction. The man catches it and punts it away.
The dog, E-Buzz, does not die and is never in danger. We see a dead canary for a few minutes but since it is dead from the beginning of the film we are not counting it.