Line 18 muffin cups with paper or foil liners. Lightly spray the liners with vegetable oil spray.
In a food processor, combine the flour, brown sugar, baking powder, baking soda, salt, cinnamon, allspice, cloves, and 1/2 teaspoons of the nutmeg and pulse to blend. Transfer to a large bowl.
In a medium bowl, whisk the eggs, yogurt, butter, applesauce, and vanilla. Fold the yogurt mixture into the dry ingredients until just blended.
Spoon the batter into the prepared muffin cups. Sprinkle the granulated sugar and remaining 1/4 teaspoons over the muffins. Bake for 18 minutes, until the muffins are springy; let cool in the pans for 5 minutes, then transfer to a wire rack. Serve warm or at room temperature.