How to Make It
Make the cupcakes: Heat oven to 350° F with the racks in the middle and top positions. Line a standard 12-cup muffin tin with paper liners. Whisk together the graham cracker crumbs, flour, baking powder, and salt in a medium bowl.
Beat the butter and sugar in a separate bowl with an electric mixer on medium-high until light and fluffy, 2 to 3 minutes. Beat in the eggs, one at a time, then the vanilla, scraping down the sides of the bowl as necessary. Reduce mixer speed to low and add the dry ingredients and milk alternately, beginning and ending with the dry ingredients and mixing well between additions. Mix until just combined.
Divide the batter among the muffin cups. Bake, on the middle rack, rotating once, until a toothpick inserted in the center of a cupcake comes out clean, 20 to 24 minutes. Cool in the tin for 10 minutes; transfer to a wire rack to cool completely.
Make the ganache: Meanwhile, bring the cream to a boil in a small pot. Remove from heat, add the chocolate, and let sit for 5 minutes. Whisk to combine. Let cool slightly.
Make the topping: Place the marshmallows on a parchment-lined baking sheet, 2½ inches apart. Bake on the top rack until golden and deflated, 6 to 10 minutes. Let cool.
Assemble the cupcakes: Divide the ganache among the cupcakes, then top each with a toasted marshmallow. Let sit until the ganache is almost firm to the touch, 15 to 20 minutes, before serving.