For the graham cracker cake: Preheat the oven to 350 degrees F. Line 12 standard muffin cups with paper liners.
Whisk together the graham crumbs, flour, baking powder and salt in a medium bowl. Beat the sugar and butter together in the bowl of an electric mixer until light and fluffy. Add the eggs one at a time, beating to blend between additions. Beat in the vanilla.
Add the graham-cracker mixture in 3 additions, alternating with the milk in 2 additions, beginning and ending with the graham-cracker mixture.
Divide the batter among the muffin cups. Bake until a tester inserted into the center comes out clean, about 22 minutes. Transfer to a rack and cool completely.
For the ganache: Place the chocolate in a medium bowl. Bring the cream just to a boil in a small saucepan, and then pour over the chocolate. Let stand for 1 minute, and then stir until smooth. Let cool until lukewarm.
For assembling: Push an apple corer about 1 inch into the top of each cupcake, removing the cake and forming a hole.
Spoon 3/4 cup marshmallow creme into a piping bag and pipe into the holes. Spread 2 teaspoons ganache over each cupcake. Let stand at room temperature for at least 8 hours.
Heat the broiler to low. Coat a rimmed baking sheet with nonstick spray. Spoon dollops of marshmallow creme onto the sheet, and then broil until slightly charred, 1 to 2 minutes. Be sure to keep an eye on them the entire time, as they will brown very quickly.
Spoon a dollop of charred creme over each cupcake and garnish with a piece of graham cracker.