Preheat your oven to 350°F (175°C) and prepare a muffin tin by lining it with paper liners or greasing each cup.
In a large mixing bowl, combine the canned pumpkin puree, honey (or maple syrup), unsweetened applesauce, eggs, and pure vanilla extract. Whisk until creamy and smooth.
In another bowl, sift together the whole wheat flour, baking soda, baking powder, ground cinnamon, ground ginger, ground nutmeg, ground cloves, and salt.
Gradually add the dry ingredient mixture to the wet ingredients, stirring gently until just combined.
If desired, gently fold in the chopped walnuts or pecans and dark chocolate chips.
Divide the batter evenly among the muffin cups, filling each about ¾ full.
Bake for 18-20 minutes, checking for doneness with a toothpick.
Let the muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely.
Notes
Serve warm and consider dusting with powdered sugar or drizzling honey for added sweetness.