Space 1889 Interestingly and perfectly logically averted. First contact in the world of Space 1889 is not something that has given rise to much existential questions about the nature of humanity. The colonial powers have treated Mars as another area to trade with and colonize and Martians as another type of native. Humans consider the human-like Canal and Hill Martians to have value near or just like a human. By trying to convert them to Christianity, for instance, they indirectly admit that Martians have souls and need salvation. This reaction is actually perfectly logical. To the average, fairly racist late Victorian European mind it is a small concession to admit that someone has a soul and a value near human. There are, after all, plenty of next-to-worthless humans (in their racist minds). Recognizing Martians as equal to white Europeans would be a completely different matter.
The value of nonhuman life is often very low in Heroic Fantasy, particularly so in Dungeons & Dragons, in which "savage" humanoids such as orcs or goblins get slaughtered en masse. In Tolkien, orcs were practically evil-shaped-like-a-man, so it can be excused, but in D&D they're just another species whose culture happens to be at odds with humans'. The game's 3rd Edition had downplayed this, going to greater lengths to give humanoids distinctive cultures and making them fully playable races. (Most campaigns still mow them down by the hundreds, though.) The 4th edition, while adding new exotic races like living constructs and dragonkin, had temporarily removed half-orcs, among other things, from the playable races. See Always Chaotic Evil. Human life has little to no value as well.
This may arguably be in part because the game system, owing to its historical wargame roots, makes killing opposing combatants the default way of dealing with them. Nonlethal and especially unarmed attacks tend to get significantly penalized in any edition of the game.
Taken to a hilariously hypocritical point in the 3.5 edition add-on Book Of Exalted Deeds, with the Vow of Nonviolence. In order to get a bonuses in certain areas, the character takes a sacred vow to never kill a humanoid or monstrous humanoid, if it can be helped. Okay, there's just one problem: humanoid and monstrous humanoid protects orcs and humans and elves and so on. Know what it doesn't protect? Angels, planetouched and elans (both are which ARE humans, but don't have the humanoid type), dragons (over half of which are more good than angels), and, you guessed it, puppies. Also there's the tiny fact that this feat stipulates that if an opponent refuses to surrender, your allies are allowed to kill them with no penalty. So there's the ultimate godly forgiveness... and no need to apply it to the people who honestly believe differently than you, and you can still beat anything with more than two hands and two legs.
As an Exalted Feat, it does prevent you from committing evil acts, such as killing Good Dragons and Angels. Elans and Planetouched were probably supposed to be protected, but have the bad luck of being created before the "Augmented Humanoid" type was made.
Lords Of Madness tops the BoED in this specific regard. It starts with lumping things into never-before-seenMeta Origin and continues with "Aberration Hunter" idea and corresponding magic effects. Given that Aberration is a type where all monsters not fitting into others can be piled at will (though one can squirrel away cute ones into Magic Beast) and 3rd edition adds an Mix And Mash Worlds to the old D&D Mix-and-Match Critters tradition, the whole picture is rather... funny: The Multiverse rightfully belongs to the humanoids and knows it. That's after AD&D Monster Manuals where everything has "Ecology" entry. The concept soon got mocked in Nodwick. Subverted in 4e, when it is given a passing mention that one of Kord's Exalted (No not that, it's kind of like a D&D version of a saint) is a Beholder.
Most of the more specific settings are better about this. In Eberron, for example, (nearly) all aberrations are creations of the daelkyr, and most of them are corruptions of normal species (though not necessarily species from the titular planet; the daelkyr have been at this for a while).
This whole concept can actually be subverted in fantasy games like D&D, believe it or not. What most critics seem to forget is that the orcs, goblins and other Mook races that are killed by the dozens are typically murderous killers who rob, kill and slaughter the humans and other "good" races first. Any treasure they have they typically got by murdering its rightful owners and stealing it in the first place. When you kill orcs and goblins and "steal" their treasure, you're typically avenging the orcs' and goblins' victims and taking the treasure back to the civilization that originally produced the wealth in the first place. The orcs and goblins are the ones who end up starting the fight in the first place!
With that said, there are many races out there that don't look human at all and are in fact quite good in alignment. Killing them is generally viewed as a bad thing for player characters to do.
In one particular Living Greyhawk Veluna event a city of sentient illusions was discovered. This led to a lengthy discussion both in and out of character by many players, continuing in discussions of the event on internet chat communities, concerning whether or not the illusions destroyed were "people".
Early on, the fact that the Ravenloft setting is evidently an artificial creation of the Dark Powers caused some gamers to argue that, if the domains weren't "real", then neither are the people who live there: that other than Mist-napped outlanders, everyone in the setting was only a construct and could be killed with impunity. Having Feast of Goblyns, the first published adventure for the setting, involve the creation and dissolution of a populated domain, due to the PCs' own actions, did nothing to clear up this Moral Dissonance.
Debates of this sort eventually quieted down after the Domains of Dread hardback and 3E products from Arthaus made playing natives of the Land of Mists more common. Guess nobody wants their player character to be branded "only a construct".
The old Marvel Super Heroes game from the '80s replaced the experience systems with a "Karma" system that rewarded heroes for doing heroic things, and penalized them for being unheroic. Killing a living person reset you to zero. But robots didn't count, so you could kill them all you wanted. Problem was, people like The Vision or Machine Man were also counted as robots. So you could gun down the Vision without penalty, unless you nicked the Scarlet Witch in the process. (This was clarified in a supplement to mean non-sentient robots, but by then the damage was done.)
Warhammer 40,000 deals with this quite handily - anything that isn't human must be purged with flame. Or humans who vary too far from the flawless ideal. And anything human that has talked to anything non-human. Or looked at it too long. Or any human that won't worship the Emperor. Or anyone who condones the above. Even if you are considered human still, your individual death generally won't miff the higher-ups in the Imperium - not having died fighting is probably considered much worse to the military.
Sure, but being all the grim and all, it's clearly stated in the novels of Ciaphas Cain that commissars who mistreat their troops (to give an specific example) don't last longer, since they usually end as victims of friendly fire. Seriously. Humans maybe be cannon fodder, but they still have enough sense of preservation and justice to know when something is going really wrong, and they would rebel against incompetent and corrupt governors and commanders, even the own Inquisition have shown that those too trigger-happy and eager to use Exterminatus will sooner or later have to answer for their actions.
The SpaceMarines are discussed by fans on whether they are actually human, due to their being genetically-engineered and mentally conditioned toward their duty of serving the Imperium (mostly by fighting), both of which essentially makes them superhuman on the battlefield at the very least - though casualties are usually not brought up (you know, being Warhammer 40000).
Population of the Imperium considers Space Marines more like legendary figures send by the Emperor himself, which means they are actually seen by the average imperial citizen as better than any other human (and respectfuly feared).
In False Gods, a Titan commander responds to a general alert by saying that he'd be opening fire if he was with the Imperial Army, but wasn't going to risk it for Marines.
Then again, every race in Warhammer 40000 thinks the same way. Even the "idiotic to the point of hilarity" orks. What measure is a non ork, anyone?
Well, these Orks ARE made of fungus after all... It's harder to garner player sympathy when one can replace himself a hundred times over by scratching his chin to flake off his skin. And to the credit of the Orks, they aren't about to change anyone's preconceptions. (Going by Deth Squadron, and how they are with each other, and how they handle death, treating them any other way would probably offend them and just cause them to WAAUUGGH! harder.) In general, Orks and Necrons are purely walking "Shoot Me!" signs. That can shoot back. A lot.
The Eldar are willing to sacrifice millions of human lives to protect their Craftworlds. They are a Dying Race, but they do go to extremes.
Despite Flanderization, the Craftworld Eldar actually avert this. Canon Black Library novels show that they do consider the moral ramifications of wiping out entire human worlds to save only a few of their own... very briefly. Mostly, pragmatism wins out.
The Dark Eldar also avert this, but in a much more sinister way, naturally. They enslave, rape, torture and kill members of the "lesser races" in realspace, but they'll happily do the same to Craftworlders, Exodites and even other Dark Eldar to further themselves if the opportunity ever presents itself, in fact they get a special kick out of defiling fellow Eldar. They do this to feed on the misery and suffering of others, in order to replenish their souls, which are being slowly drained by the Chaos God Slaanesh. Slaanesh also claims their souls upon death. In their eyes, all sentient life is equal. Equally worthless.
Inverted by the Chaos Gods, who prefer Humans specifically because they're easier to corrupt than the other races of the galaxy. Only Slaanesh has a focus outside of humans, and that is because the Eldar squicked him into existence and are now irrecoverably tied to him (hence why Eldar of all walks fear death).
In Ex Tempore, most of the inhabitants of Ex consider the lives of the people of the Circle (A.K.A. us) to be merely tools in observational experiments. After all, all time in Orbis can be seen from Ex, as if we were frozen. How real can we be, anyway?
Oddly Averted with ONI form AT-43 whose legions of sentient Zombines are still on payroll and still move up the ladder. In fact one of the back story talks about a number of PR stunts (after the nonsentient ones messed things up) included a successful cartoon about a Super Zombine hero and one of Oni's main heroes marring one it worked so well that a number of still living people wished to be made into Zombines.
The Fetches from Changeling: The Lost are an interesting case. They're magical fae creations made to replace the characters snatched by the Gentry, but depending on how well the Fetch is made it can range from a sociopathic monster to a decent moral creature that has no idea what it really is. Killing a Fetch damages a Changeling's Clarity, but also provides the changeling with a portion of his/her lost soul. It's really hard to reclaim your old life when your friends and family don't realize you've ever been gone, and can cause all sorts of complications because it might not be immediately obvious if your Fetch is a decent person, a screwed-up person, a sociopath, or a spy for the Gentry. The material implies that most Changelings kill their Fetch when they return (or hire other Changelings known as Jack Ketches to do the deed in their place), but reactions range all over the scale.
Averting this trope — i.e. treating your own and other characters as if they're real beings whose lives have importance, not imagined proxies in a recreational fantasy — is a big part of what "deep role-playing" is all about. Conversely, "metagaming" invokes it deliberately, treating characters as mechanisms for scoring points and achieving game-objectives.
In Palladium's RIFTS setting, the Coalition States have genocidal desires towards D-Bees. This trope gets invoked because many players come to sympathise with this goal due to the fact that, really, it seems like eight or nine out of ten D-Bees areAlways Chaotic Evil.
In Genius: The Transgression all intelligent life is explicitly equal (even though most of the non-human life technically don't exist... reality is complicated). Plenty of characters have different opinions, which is reflected in their declining Karma Meter.