We borrowed the filling from a favorite holiday pie and baked it on top of a spiced cupcake for these rustic, all-American bites. The tops spread a bit, so use a spoon or a small offset spatula to help lift the cupcakes out of the pan.
For the filling: Toss the apples, granulated sugar, lemon juice, cinnamon and salt together in a medium bowl. Melt the butter in a medium skillet over medium heat. Add the apples, and cook, stirring frequently, until the apples are tender but still pliable and the liquid is simmering, about 6 minutes. Add the flour, and stir until it dissolves and the liquid thickens. Remove the skillet from the heat, and let the filling cool completely. Divide the filling evenly into 12 little packed mounds; set aside.
For the cupcakes: Position an oven rack in the center of the oven, and preheat to 350 degrees F. Line a 12-cup muffin tin with paper liners, and coat the liners and the top of the tin with cooking spray.
Whisk the flour, baking powder, cinnamon, nutmeg and salt together in a medium bowl. Beat the sugar and eggs in another medium bowl with an electric mixer on medium-high speed until light and creamy, about 2 minutes. While continuing to beat, gradually pour in the butter, then add the vanilla. Adjust the mixer to medium-low, and add half the flour mixture. Add the milk, then the remaining flour mixture, taking care not to overmix the batter. It will be thin, like pancake batter; transfer it to a liquid measuring cup to make filling the muffin cup easier.
Divide the batter evenly among the cups of the prepared muffin tin. Top each with a mound of apple filling. Bake for 15 minutes (the cupcakes will spread quite a bit). Remove the tin from the oven, gently brush the tops with melted butter and sprinkle with granulated sugar. Continue to bake until the tops of the cupcakes, which bake and puff around the apple filling, spring back when pressed, 6 to 8 minutes more. Let the cupcakes cool in the tin for a few minutes, then transfer to a rack to cool completely.
For the whipped topping: Beat the cream, confectioners' sugar and sour cream in a medium bowl with an electric mixer on medium-high speed until the mixture forms soft peaks. Transfer it to a pastry bag or a resealable plastic bag (snip off the tip). Pipe a dollop of whipped topping onto each cupcake (don't completely hide the cupcake), and sprinkle with cinnamon.