Well considering we know nothing about the game itself, it's hard to answer coherently. A koopatroopa would look kind of out of place in silent hill...
Generally speaking then, try to use monsters as narrative devices, not only obstacles to be overcome by the player: giv'em some personality, and make the reflect bigger aspects of the plot. Some might be bond to a certain environment, like wild animals or primitive humanoids. Other may rather reflect their evil master's will: footsoldiers of a warlord, or the undead servants of a necromancer. Some might be outcast, evidently out of their normal element, like, say, aggressive aliens shipwrecked in a prehistoric jungle, or whatever. The individual story of each particular kind of enemy it's not that important, they are only stubs that should help to better picture the whole setting of the game.
It's a very fashionable, post-modern thing to make some cross-references in nowadays games (and series, movies or films). That's FF's Odin, Bahamut or Shiva. I've lost the count of how many Niflhaims or Yggdrasils are out there. From myth to cryptozoology, we humans've always been good imagining monsters. Lovecraft is also a great source of unspeakable inspiration, but pop culture is vast and full of terrors. Why not include morlocks, graboids, triffids or kaijus? They're all creatures with their own lore, which of course you may ignore completely (as Indian Shiva was no ice goddess) or adapt to your own fluff.
PS: interesting resources, mystazsea , i'll have a good read. But see, there's Niflheim again. Godammit.