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).
My Little Unicorn: Pony version. 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.
