Preheat oven to 350℉. Prepare a standard cupcake pan with liners and spray them with cooking spray. Set aside.
In a large mixing bowl, whisk cake mix, ginger, cinnamon, cloves, and nutmeg.
Add molasses, eggnog, oil, and eggs. Blend the wet ingredients with the dry on medium speed until fully combined and smooth.
Using a large cookie scoop, fill each cupcake well, about ½ full, just under ¼ cup per cupcake.
Bake for 16-18 minutes until a toothpick comes out clean or the top of the cupcake springs back when lightly pressed.
Remove the cupcakes from the oven and cool them in the pan for about 5 minutes. Transfer to a wire rack to cool completely before frosting.
While the cupcakes are cooling, beat the cream cheese and softened butter in a large bowl until fluffy.
Add powdered sugar, vanilla extract, and eggnog, a little bit at a time, and until the frosting is desired consistency.
Frost or pipe onto cooled cupcakes. Dust with nutmeg, or decorate with festive sprinkles or gingerbread cookies.