i've actually thought a little about this as well...not so much about where they come from, but the notion that these symbols all seem to be neutral sources of power. MOTU has always had this idea that power is just power...it is not good or evil...it is only the intent of the user that makes it good or evil.
the universe is power...neutral power...but a master of the universe can be good or evil.
take the snake for example. for the snake-men, it represents the superiority of their race, but the goddess and teela both use the snake for good. the skull is another symbol like this.
i think most of these totems got their start with eternian tribes. we know that king grayskull used a skull as a symbol and rode a lion in battle. his wife, queen veena, used a bird of prey as a totem, which probably originated with her own tribal ancestry.