I could definitely see using the mythos -- although probably not by that name, since it's too familiar and not mysterious enough for most players -- in Alien or Mothership, for instance.
Coming across a blasted alien ruin of a planet that's apparently uninhabited, but there's signs that something big is alive beneath the black waters of the great pool central to the extinct alien society's temple city, and the PCs slowly translating the writings on the ruins to say that there's an alien god slumbering there who will devour all life if he awakes? Now we're cooking. (For the record, I think this is what Prometheus was trying to achieve, in its clumsy way.)