"which one" is: out of A, B, C,... which one of these is your favorite? "what is" is: out of every movie ever, what is your favorite?

Thank you Dana :D

In general "What is your favorite movie?" is correct. "Which (one) is your favorite movie?" is correct if you give the person a list of movies to choose from. For example: "I have the movies Shrek, Home Alone, and iRobot. Which one is your favorite?"