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1. Preheat oven to 350 degrees. Line 24 cupcake cups with paper liners.
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2. Sift the flour, cocoa, baking powder, baking soda and salt together; set aside. In a separate bowl, stir together the yogurt, pumpkin, vinegar, and vanilla extract, set aside.
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3. In a large mixing bowl, and using an electric mixer on medium speed, beat butter and brown sugar until light and fluffy. Beat in the eggs, one at a time. Alternately beat in the flour and pumpkin mixtures in thirds (for example, beat in 1/3 flour mixture followed by 1/3 pumpkin mixture and repeat until everything is combined). Fold in the mini chocolate chips.
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4. Working quickly, spoon batter into cupcake cups, filling each about 3/4 full. Place cupcake pans in the center of the preheated 350 degree oven and bake approximately 25 minutes. Cupcakes are done when they spring back when lightly touched or a toothpick inserted in the center comes out clean. Cool pans on wire racks for 10 minutes then remove cupcakes from pans and let cool completely on the wire racks.
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5. While cupcakes are cooling, prepare cream cheese frosting (recipe follows). When cupcakes are completely cool, spread with frosting.
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6. In a medium bowl, beat together cream cheese, butter, powdered sugar, vanilla, cinnamon, and nutmeg. If frosting is too soft, chill in fridge for 15-20 minutes.
