Preheat the oven to 350° F. Line two cupcake pans with paper liners. (I found that using tinfoil liners worked better when it came time to torch. The paper burned a little.) In a small mixing bowl, combine the graham cracker crumbs, sugar, and melted butter. Mix well with a fork. Drop about 1 tablespoon of the graham cracker mixture in the bottom of each cupcake liner and press down to line the bottom. (Note: I found the bottom of my squeeze bottle to be the perfect size to do this job neatly and quickly.) Sprinkle a small amount of the chopped chocolate on top of the graham cracker crusts. Bake for 5 minutes. Remove from the oven and maintain the oven temperature.
To make the cake batter, sift together the sugar, flour, cocoa powder, baking powder, baking soda, and salt in the bowl of an electric mixer fitted with the paddle attachment. Mix on low speed just to combine. In a small bowl, combine the eggs, milk, vegetable oil, and vanilla extract and whisk together. Add to the dry ingredients and mix on low speed for 30 seconds. Scrape down the sides of the bowl, then beat on medium speed for 2 minutes. Add the boiling water and stir just to combine. The batter will be thin.
Divide the batter evenly between the prepared cupcake liners, filling each about ¾ of the way full. Return the pans to the oven and bake about 18-20 minutes, until a toothpick inserted in the center comes out clean, rotating the pans halfway through baking. Allow to cool in the pans 5-10 minutes, then remove and transfer to a wire rack to cool completely.
To make the frosting, combine the egg whites, sugar, and cream of tartar in the top of a double boiler. Heat the mixture, whisking frequently, until it reaches 160° F with an instant-read thermometer. Transfer the mixture to the bowl of an electric mixer fitted with the whisk attachment. Whisk starting at low speed and gradually increasing to medium-high speed until stiff, glossy peaks form. Mix in the vanilla until combined. Frost cooled cupcakes as desired. Brown with a kitchen torch and garnish with chocolate or graham cracker segments.