Mix together in a large bowl all-purpose and whole wheat flours, sugar, cinnamon, baking powder, baking soda and salt.
In another medium or large bowl, whisk together eggs, apple butter, oil and vanilla extract
Stir in grated carrots and apples.
Make a well in dry ingredients and stir in the wet ingredients until just combined. (The batter will be very stiff.) Coat 18 muffin cups with cooking spray. Spoon the batter into prepared muffin cups, filling them about three-fourths full. Combine topping mixture in a small bowl; sprinkle over the muffin tops. Topping:
Melt butter in a microwaveable bowl and mix in brown sugar walnuts or pecans and toasted wheat germ.
Bake muffins about 20-25 minutes, until the tops turn golden brown and spring back when touched lightly. Cool for 5 minutes in pans, then loosen edges and turn muffins out onto a wire rack to cool.