Gunnerkrigg Court is a brilliant amalgam of fantasy and mythology, and many of the characters and story elements come straight out of myths. While Coyote himself is obviously the Native American trickster-hero, I can't find any mythology related to the GC story of his creation of the glass-eyed men. Does that plot element come out of any particular legend, or is it solely within the GC universe?
The Maidu creation myth contains the following passage, explaining how Coyote tried to make people but laughed, therefore creating the glassy-eyed people that we know as Shadow People in Gunnerkrigg Court (thanks to @Brandan Long for the Gunnerkrigg ref):
When Coyote had seen the two people, he asked Earth-Initiate how he had made them. When he was told, he thought, "That is not difficult. I'll do it myself." He did just as Earth-Initiate had told him, but could not help laughing, when, early in the morning, the woman poked him in the ribs.
As a result of his failing to keep still, the people were glass-eyed. Earth- Initiate said, "I told you not to laugh," but Coyote declared he had not. This was the first lie.