Preheat oven to 400 F. Grease a muffin pan with non-stick spray or use paper liners. In a large mixing bowl, combine the brown sugar, eggs, and oil. Stir for about 2 minutes using a wooden spoon or electric mixer. Add the pumpkin puree to this mixture and stir for another minute.

In a separate mixing bowl, combine the flours, baking soda, baking powder, cinnamon, salt and nutmeg. (If using flax seed or wheat germ add at this point.) Add the dry mixture to the wet mixture a little bit at a time until fully combined. Stir in the chocolate chips and then divide batter evenly among muffin cups. Top with more chocolate chips if desired. Bake for 15-18 minutes.