Preheat oven to 375 degrees F (190 degrees C). Lightly oil 18 muffin cups, or coat with nonstick cooking spray.
In a medium bowl, whisk together eggs, egg whites, apple butter, oil and vanilla.
In a large bowl, stir together flours, sugar, cinnamon, baking powder, baking soda and salt. Stir in carrots, apples and raisins. Stir in apple butter mixture until just moistened. Spoon the batter into the prepared muffin cups, filling them about 3/4 full.
In a small bowl, combine walnuts and wheat germ; sprinkle over the muffin tops.
Bake at 375 degrees F (190 degrees C) for 15 to 20 minutes, or until the tops are golden and spring back when lightly pressed.