Many Bleach fics touch on this, but especially, Downfall engages this head-on. Unohana treats Hollows with dignity and respect, and as a result, most of the more humane examples gravitate towards her. More importantly, Aizen, of all people, questions Soul Society's "Kill 'em all" mindset. Of course he's a good guy this time around but that's par for the course. The way the war is shaping up, many of the main characters will be forced to confront this concept.
Naruto fanfics tend to go into this regarding the jinchuuriki.
An important plot point in It's not the Raptor DNA is that Elise has human self-awareness and the ability to feel empathy, even communicate with humans through sign language. Many characters in the story question the morality of her being owned by a company and used as an attraction in Jurassic World.
A number of Axis Powers Hetalia fics go into this, in regards to the Nations' Ambiguously Human status and whether or not they do terrible things out of a genuine desire to do so or because they are under their bosses' control. Some, like Human Curiosity, have humans use the Nations for experimentation (and in said fic, one human character speculates that the feelings and actions of the Nations are only reflections of their people, meaning they have no personalities or thoughts of their own and thus are not human).
Ching smiled. “I’m active duty Navy. I’ve got a whole set of combat implants and nanoware boosters. On top of that, you’reHomo Sapiens, I’m Homo Avalonis. It not really a fair contest. Even without my military gear, I could outrun cheetahs without much trouble.” “You’re not even human? No fair. And I was already tired, too.” Ching gave her a sharp look. “’If you prick us, do we not bleed? If you tickle us, do we not laugh? If you poison us, do we not die? And if you wrong us, shall we not revenge?’ I’m human, Asuka, I’m just not Homo Sapiens. Mere species is neither the measure nor definition of humanity here. Human is as human does. There are plenty of people on this planet alone who don’t have even a single codon of Homo Sapiens DNA in them, but are very human. And you know damn well there are plenty of people walking around on your world that are one hundred percent Homo Sapiens that are not human in the least. Be careful, some might take what you said as rather an insult.” Asuka was a bit taken aback by Ching’s sharp tone. “Sorry.”
Pony version in My Little Unicorn. Titan's henchponies are artificial beings and considered not worth rescuing by the heroes when the reality they fought in starts to collapse around them and they are too weak to escape.
A major theme in Unwanted Free Ugly Troll and Loophole. Trolls are shown to be fully capable of thought and emotion, yet are treated as pets and have few rights — one of the goals of the protagonists of both stories is to change this attitude. Loophole, especially, plays this for all the Tear Jerker it's worth; Vriska, a former fighting troll, is viewed as a savage monster by most, when she's really just a scared little girl. She is eventually euthanized by court order.
In the Tamers Forever Series DC breifly questions whether it's right for him to kill a wild Cyclonemon, seeing as how it's only trying to survive. However, he soon decides "it's either him or me".
In Friendship Is Optimal, Celest-A.I. has no regard whatsoever for non-human life since she hasn't been programmed with any, and will readily destroy anything non-human she encounters to turn it into more computing resources.
In the Buffy the Vampire Slayer story Spy Game, members of the Watcher Council are horrified that Xander would kill a human necromancer that was raising an army of zombies but aren't remotely bothered they slaughtered an entire village of Kwaini (a race of universally non-violent demons). That is, until they learn said Kwaini were considered German citizens and now the government wants answers.
Throughout the first four acts of the fic, the angels consider all monsters automatically evil: upon death, monsters are automatically sent to Limbo, whereas demons such as Kurumu and Dark are sent to Hell by default. In fact, Rason was nearly executed for murdering an evil human man that was about to rape a good monster girl, but one of the elders instead elected to give Rason a chance to prove that monsters can be good by having him exiled and sent to Yokai Academy. On another side, in Act IV chapter 16, they outright state that, even if Hokuto is a monster now, he is still considered human in their eyes because he was born a human. As of the end of Act IV, the angels have accepted that monsters can be good to, and arrange for some to be sent to Heaven.
In Acts V and VI, the Human Defense Agency, a Creature-Hunter Organization founded in the wake of The Unmasqued World, is rather quick to write off all monsters as evil, even believing that the monsters orchestrated Alucard's resurrection just so they could kill him and make themselves look like heroes; one HDA soldier in particular outright tells Moka and Akasha to their faces that he doesn't even consider monsters animals. On two different occasions, members of the HDA ask if they can guarantee that no further monster attacks will happen; as is pointed out, they can't guarantee it because monsters have free will just like humans, with Akasha remarking that perhaps monsters wouldn't be so eager to attack humans if the HDA didn't constantly threaten them.
A key factor throughout the entire series is that Tsukune and co. constantly argue that "a life is a life, no matter what it is." In short, they themselves value all life, human and monster alike.
In Shinji's Nightmare, Shinji calls out the adults for disregarding his ideas and opinions on his new form after he's become an Alicorn. Such as his desire to stop eating vegetables all the time as his form is clearly an omnivore, only for them to insist "Horses don't eat meat Shinji."
An important theme for the four in The Keys Stand Alone, inasmuch as they pretty much regard everything with a brain and a face, and even large plants, as Things Not To Be Harmed. To the point where they get into trouble because they refuse to harm monsters that everyone else gladly slaughters. (Mind you, a war is more or less taking place, but they're there involuntarily.)