Preheat the oven to 350 degrees F. Line cupcake pans with 18 liners.
In a medium bowl, whisk together the flour, cocoa powder, baking soda, baking powder and salt. Using an electric mixer with the paddle attachment, cream the butter until smooth. Gradually add the granulated sugar about 1/4 cup at a time until the mixture is light and fluffy, scraping down the sides of the bowl occasionally. Add the eggs, one at a time, beating well after each addition. Add the vanilla. Alternately add the flour mixture and the milk, starting and ending with the flour mixture, beating well after each addition and scraping down the sides of the bowl occasionally.
Spoon the batter into the liners. Bake until a toothpick inserted in the center comes out clean, 16 to 18 minutes. Cool the cupcakes completely.
Make a hole in the center of each cupcake using a small paring knife or apple corer, making sure not to go all the way to the bottom. Pipe the Dark Chocolate Filling into each cupcake all the way to the top, reserving some for garnish. Frost the cupcakes with Peanut Butter Frosting, reserving some for garnish. Roll the edges of the cupcakes in mini chocolate chips. Drizzle the cupcakes with the remaining chocolate filling, and then with the remaining peanut butter frosting.
Place the chopped chocolate in a small bowl. In a small saucepan, heat the heavy cream over low heat until it simmers. Remove from the heat and pour over the chocolate pieces. Add the butter and let stand for 1 minute. Stir until smooth. Let cool slightly. Cut 1/8-inch off the end of a piping bag. Pour the mixture into the piping bag.
In a large mixing bowl, using an electric mixer with paddle attachment, whip the cream cheese on high speed about 30 seconds until smooth. Add the peanut butter and continue mixing on high speed for 1 minute until well blended, scraping down the sides often. Add the vanilla. On low speed, add the powdered sugar 1/2 cup at a time.
This recipe was created by a contestant during a cooking competition. It has not been tested for home use.