Position a rack in the center of the oven and preheat to 350 degrees. Place paper liners in two 12-cup muffin pans.
Prepare the cupcakes: Sift together the flour, baking soda, baking powder and salt in a bowl. Bring the sugar and 1 cup water to a boil in a saucepan, stirring until the sugar dissolves, about 3 minutes. Pour into a large bowl; add the chocolate and butter and let sit, stirring occasionally, until the chocolate is melted and the mixture has cooled slightly. Stir in the vanilla. Using a mixer, beat in the eggs, then mix in the dry ingredients.
Divide the batter evenly between the prepared pans (about 1/4 cup batter per cupcake) and bake until a toothpick inserted in the center comes out clean, about 25 minutes. Cool in the pans for about 25 minutes, then transfer cupcakes to a rack to cool completely.
Meanwhile, prepare the filling: Using a mixer, cream the butter until light and fluffy. Beat in 1/2 cup confectioners' sugar. Add the vanilla and 1 tablespoon heavy cream; beat until smooth. Beat in the remaining 1/2 cup confectioners' sugar and 2 tablespoons heavy cream in batches, alternating after each addition. Beat in the marshmallow creme; set aside.
Prepare the ganache: Place the chocolate in a stainless-steel bowl. Heat the cream and 1 tablespoon butter until just boiling, then pour over the chocolate; let stand for 5 minutes. Whisk until smooth. Add 2 teaspoons vanilla; let stand until cool but still glossy and liquid.
Spoon the filling into a pastry bag with a medium tip. Insert the tip into the center of each cupcake top; fill until the cupcake is heavier (do not overfill). Dip the cupcake tops in the ganache. Chill for at least 15 minutes.
Meanwhile, prepare the icing: Using a mixer, beat the remaining 1 stick butter, 1/4 teaspoon vanilla, the milk and confectioners' sugar until smooth. Spoon into a pastry bag with a small tip; pipe onto the cupcakes to decorate.