The episode's title is a combination of the names to the McDonald's breakfast sandwich the Egg McMuffin and the MacGuffin, a plot device made famous by Alfred Hitchcock.
When Nate reveals Ray's fate, Mallus' theme from Season 3 plays in the background.
Gary picks up a book with a Flamel Cross in the cover. While the concept of the cross is part of alchemical tradition, the specific design is the one from Fullmetal Alchemist.
The dress Zari wears in 1933 New York is identical to that worn by Karen Allen as "Marion" in the original "Indiana Jones", yet another Easter Egg from the older movie.
The Adventurers society seems to be an allusion to the Explorer's Club in New York City.