The Message Catholic Edition version of the Book of Judith has "Are you there, God? It's me, Judith."
The fourth Captain Underpants novel has the chapter title "Are You There, God? It's Us, Fluffy and Cheeseball". note The villain of the book forced George and Harold to change their names to "Fluffy" and "Cheeseball" respectively.
Jacqueline Wilson has Ali from The Other Side reading the book and, upon reflecting, thinks that Margaret is making a major deal out of nothing really major, seeing as she has good friends, great parents, and even good grandparents.
In Scrubs, Dr. Cox (who always calls JD by girls' names) says in one episode, "What in the name of 'Are You There God, It's Me Margaret' were you thinking?"
Ted Lasso: In "Beard After Hours", when Beard prays in a church while taking shelter from the rain, he opens his prayer with "Are you there, God? It's me, Margaret's little boy".