Anathema (the witch) riding her bicycle referenced Margaret Hamilton (as Almira Gulch, who becomes a witch) riding her bicycle. Both bikes had baskets and the music is similar, as well.
The stripes and colors of Newt's knitted tie are a direct homage to the very long scarf of Tom Baker's Fourth Doctor, a predecessor of David Tennant's Tenth Doctor in the Doctor Whoniverse.
One of Adam's friends has the middle name "Moonchild" which is what Bastian names the Childlike Princess. The ultimate origin of the name is from Aleister Crowley.
The series title is a pun on that of the "Omen" and follows the adventures of a child Antichrist and his hell hound, which turns out not to be a rottweiler.