The title Into The Woods is a reference to a musical about fairy tales, including Cinderella. In this episode the Penguin is placed in the position of working as a servant in his deceased father's house, serving his step-mother and step-siblings, just like Cinderella.
Near the end of the episode, Selina throws her coat - the one Bruce had repaired for her, but just before she does, they show the stitches Bruce made. This is clearly a foreshadowing of the cat costume worn by Michelle Pfeiffer in Batman Returns.