There is an invisible value placed on the existence of non-human characters in fiction, compared to the value of the life of a human. Killing/destroying one may or may not be the same thing as killing a human. The difference between Not Even Human on one end of the scale and Not Quite Human on the other can be a very fine one, and where a series chooses to draw that line can vary as wildly as the writers' imaginations.
Intelligence and emotions, and whether the character in question is actually alive in the conventional sense, are usually what dictate the morality of the situation. But more often than not, it's based upon how human-like the character is (an issue further explored in this blog post). The sliding scale usually goes something like this:
Starting with the least likely to be granted rights...
Undead beings like skeletons, zombies, ghouls, and victims of certain strains of The Virus do not blip at all in this value (despite still being Homo Sapiens). There's hardly any controversy about it either, probably because they're trying to kill you. In fact, killing one is seen as only helping along a natural process.
There are some exceptions in the very, very rare works where the zombies are not entirely mindless and retain a bit more personality and/or self-control. One example of this (albeit one that some viewers found ridiculous) is the 2008 remake of Day of the Dead. It is eventually revealed that certain zombies not only don't eat people, but are completely non-violent. Because of this, multiple characters argue over whether or not it's okay to kill them. They arezombies, but they aren't hurting anyone. More on this in the Film section.
Monsters Of The Week, GiantMonsters and Big Creepy-Crawlies are generally treated as huge pests and exterminated as such without much controversy, typically in self defense. There are some exceptions. If you are a monster, the more you resemble a more conventional specimen of the creature you are based upon, the fewer people you directly harm, and (most importantly) the more personality you have, the better your chances are for surviving. Some human or other will recognize that you are merely misunderstood and may try to help you. Of course, if you eat that human, you're pretty much boned.
Vampires, while they are technically among the undead, have variable ranges simply because they usually have more personality. Most characters can kill them anyway even if they're Technical Pacifists. Certain depictions of Batman and King Graham from King's Quest have killed off Dracula with favorable karmic results (With Graham, the Fan Remake takes a different route), even when killing anything is anathema to them. The idea here, as well as with the other undead mentioned above, may be "Well, technically, they're already dead, so it's okay! And anyway, Vampires are Always Chaotic Evil!"
Supernatural entities vary depending on alignment. Typically demons are on the same level as undead.
And then there is an uncomfortable border line occupied by characters who are human — but since they aren't "normal", they aren't considered as such. Good Cyborgs, if the brain is still intact, are almost always considered human, except by the persecutors who harass them. Bad Cyborgs are treated on the same scale as Mecha-Mooks. Other "partially disembodied" entities, whether they once were humans or were made like that run the entire spectrum from being accepted as variant humans to "kill them just to end their supposedly nightmarish existence and go drink some Brain Bleach". The same can be said for Transhuman characters.
Rubber-Forehead Aliens rarely have this problem - as their actors are obviously human, it is easy to transfer the value (this is largely why the trope persists even into the modern, CG-heavy era). Humanoid Animals and Half Human Hybrids tend to get the same protection as a normal human... but it depends on how humanlike they are. If they take up a form that isn't bipedal, rely on their instincts too much, or otherwise start toward the Talking Animal side of things, they can quickly reach the level of monsters-of-the-week.
As far as other fantastic races, it often seems that the morality of killing the race depends on how much they resemble humans either culturally or physically. Dwarves, elves, gnomes and halflings all look relatively human, and so killing them is bad, but the bestial-looking orcs, goblins and trolls are evil and should be killed. Other races who obviously are not human, but possess cultural traits such as music or clothing styles that the human audience can easily recognize or identify with, are also given preferential treatment over whatever evil races exist.