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Special equipment: a pastry bag or a large resealable plastic bag
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For the filling: Toss the apples, granulated sugar, lemon juice, cinnamon and salt together in a medium bowl.
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Melt the butter in a medium skillet over medium heat.
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Add the apples, and cook, stirring frequently, until the apples are tender but still pliable and the liquid is simmering, about 6 minutes.
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Add the flour, and stir until it dissolves and the liquid thickens.
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Remove the skillet from the heat, and let the filling cool completely.
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Divide the filling evenly into 12 little packed mounds; set aside.
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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.
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Whisk the flour, baking powder, cinnamon, nutmeg and salt together in a medium bowl.
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Beat the sugar and eggs in another medium bowl with an electric mixer on medium-high speed until light and creamy, about 2 minutes.
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While continuing to beat, gradually pour in the butter, then add the vanilla.
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Adjust the mixer to medium-low, and add half the flour mixture.
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Add the milk, then the remaining flour mixture, taking care not to overmix the batter.
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It will be thin, like pancake batter; transfer it to a liquid measuring cup to make filling the muffin cup easier.
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Divide the batter evenly among the cups of the prepared muffin tin.
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Top each with a mound of apple filling.
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Bake for 15 minutes (the cupcakes will spread quite a bit).
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Remove the tin from the oven, gently brush the tops with melted butter and sprinkle with granulated sugar.
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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.
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Let the cupcakes cool in the tin for a few minutes, then transfer to a rack to cool completely.
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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.
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Transfer it to a pastry bag or a resealable plastic bag (snip off the tip).
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Pipe a dollop of whipped topping onto each cupcake (don't completely hide the cupcake), and sprinkle with cinnamon.
