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.
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).
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.