Preheat oven to 350-degrees F. Spray 2(6-cup) muffin tins with nonstick cooking spray or use cupbcake liners. In a small saucepan, over low heat, melt the chocolate chips with butter, stirring ocassionally. Remove from heat and set aside. In a large bowl, blend flour, brown sugar, ginger, cinnamon and baking powder. Fold in eggnog, molasses, apple sauce, egg and chocolate mixture until well incorporated.
Evenly divide among the prepared muffin cups, filling each 3/4-full. Sprinkle the top of each with Kosher salt and bake 18-20 minutes, or until the center bounces back when lightly touched. Remove from oven to cool slightly before transferring to plate or rack to cool completely before frosting.
To make Smoky Caramel Frosting, add all ingredients to a bowl and beat on low until the sugar has been incorporated. Then turn the mixer on high and beat for 30 seconds, until it is as creamy as possible. Either spread with a knife dipped in water, pipe with a pastry bag or place in a resealable bag, snipping off a corner to pipe out.
Makes 12 cupcakes