Let it first be noted that when I refer to King Kong, I am referencing only the Peter Jackson movie (I'm unfamiliar with the details of any other versions), and as far as The Phantom of the Opera, I may be simultaneously thinking of the original novel and the movie based on Andrew Lloyd Webber's musical (though they're very different).
You'll notice that in both stories there arises an almost love triangle in which one of the individuals is some way or another inaccessible and the remaining two become a couple by the end. These are, of course, Christine and Raoul with the Phantom/Eric as the extra and Ann and Jack Driscoll with King Kong as the extra. The Phantom's inaccessibility is initially his deformity, but ultimately his evil nature. King Kong, on the other hand, is literally not human. He is a force of nature, a force that Man tries to control, to both their dooms. Ann is the only one who can access him on his level, trying (without success) to stop Man from harnessing and harming him. Similarly, Christine is able to feel true compassion for the Phantom; though it is Raoul she loves, she extends her sympathy and kindness toward Eric as a human being that the world will forever shun--but he has moved too far down his path to completely retract.
Raoul and Jack are both of a gentle nature; it is because of this nature that they are able to understand the perspectives of compassion Christine and Ann have chosen. Raoul only wants to marrry Christine and take her out of this labyrinth of the Phantom's Opera (oh, did I slightly steal some of the lyrics from "Why Have You Brought Me Here?"). Jack was drawn into the expedition against his will; he only prolongs it to rescue Christine and has no interest in exploitation of the wilderness. So both Christine and Ann by their compassion, ironically, drag their men into trials and danger. Even forces of good do not always produce fun results, eh?
Ultimately, the "good guy" gets the "innocent girl" and the extra character is either killed or otherwise thrown away. Is this the triumph of good over evil, or the inevitability of society's in-acceptance or destruction of forces/figures that are different from it? Or is it both? The more I look at them, the more I find that these are very similar stories.