The obvious one is Invasion of the Body Snatchers. Where Aliens grow replacements for Human beings. They look just like the person whose life they have taken over. This was clearly a metaphor for the paranoia of the Red Scare and McCarthyism. The idea that your best friend, next door neighbor, or even a family member could be secretly plotting against not just you, but the whole country.
Spalko's plan for the Skull plays into the paranoia of the time. But clearly Mac's betrayal of Indy as well. Which is compounded by the fact that Mac's true loyalties are never clear.