I played one of those Cabela games recently. A part of me died inside when I shot a bullet through a polar bear's brain. It wasn't even doing anything, it was just standing there minding its own business. Never mind that you can also hunt endangered animals.
Maybe flying though cows in any typical racing game with a country level would count. I recall you could blast away cows and pigs and chickens in Redneck Rampage too. Or getting up close to an animal in Paperboy before whacking it at full velocity with a flung newspaper... or maybe I'm the only one who did that.
I'm just glad there hasn't been a videogame version of "Oh Brother Where Art Thou" yet. You remember that one scene where the guy starts shooting cows for no reason and shortly thereafter a cow gets hit by a car. I wonder what it is with the nonchalance in killing cows. Maybe because in games they just stand there and are easy targets?
Another example could be in Black & White where you could slap your Creature if it's misbehaving. Or you could be the cruel sort and slap it hard and slap it many times. I remember doing that to the Cow in the first example where it's frightened of its new home and needs reassurance, and slapping it just makes it cry. I think the Creature weeps in other cases if it's unhappy. But in general, you can pet the Creature to praise whatever it did or slap the Creature to disapprove of what it did. And then usually do it multiple times before it finally gets it.
It seems it's abuse if they're minding their own business or they're visibly scared. But if it's in self-defense, then it's fine. Is it fine even if you were the one who provoked the animal?
"Shadow of the Colossus" seems to be built on having colossi that usually don't care about you until you start stabbing them. Many reviews have pointed out that it's a pretty sad game, that you're indiscriminately killing these colossi in an attempt to save a girl that may or may not happen. And after you kill one, you have to watch it slowly fall to the ground in a lifeless heap.
...But that one colossus had it coming, I mean, it kept attacking me when I was laying on the ground stunned, so I couldn't do anything to fight back. Cheap jerk.
Looks like we've already mentioned the loopholes when a game's characters consist of anthropomorphic animals (or "furries" if you're inclined), where I believe it doesn't really count since presumably they act more like humans in those games.