One of the most famous lines from the film is Zaius's line "Don't look for it, Taylor. You may not like what you find" about Taylor's question about how apes evolved from man. Dana Scully said a similar line to Fox Mulder in 1995, about his quest for proof of the existence of alien life. (TXF: "War of the Coprophages")
When Mulder is inhabiting the body of Morris Fletcher, Scully says "I'd kiss you if you weren' so damned ugly". In the film, Taylor asks to kiss Zira, who replies "alright, but you're so damned ugly".