For the cupcakes: Position a rack in the middle of the oven and preheat to 300 degrees F. Set liners in muffin cups.
Put the chocolate and prune juice in a microwave safe bowl. Heat in the microwave on low power, stirring occasionally, until completely melted.
Whisk the flour, sugar, cocoa powder, baking soda, baking powder, and salt in a large bowl. In another bowl, beat the egg and yolk with an electric hand mixer at high speed until slightly thick and lemon colored, about 3 minutes. Slowly add buttermilk, oil, vanilla, and melted chocolate mixture to eggs, beating until thoroughly combined. Add the flour mixture and beat until just combined.
Divide the batter among muffin tins, filling them 1/2 of the way. Bake until a toothpick inserted into the center of the cupcakes comes out clean and the tops spring back when pressed gently, about 25 minutes. Cool the cupcakes in the tin on a rack for 10 minutes then remove from the tin and cool completely.
For the frosting: Beat the butter, peanut butter, and cream cheese in a large bowl with an electric mixer until light and fluffy. Gradually add the confectioners' sugar and milk mixing until the frosting is smooth. Add food coloring as desired. Refrigerate the frosting until firm.
To decorate the cakes: For the witches hat, score a circle in the middle of a cupcake. Cut a deep cone-like shape with a knife held at an angle. Rotate the cupcake to complete the circle and remove the center. Repeat with all the cupcakes. Generously scoop or pipe enough frosting into the center of each cupcake to fill the hole and to come over the cake to make a face. Top with a chocolate wafer cookie. Put a dot of frosting in the middle of the wafer cookie and invert the cone shaped piece of cake on top to make a witches hat. Use skinny licorice, toasted coconut or cereal flakes for hair and candies for eyes and/or nose. Refrigerate for up to 30 minutes before serving.