Preheat oven to 400 degrees. Line muffin pan with paper liners.
In a large mixing bowl, whisk together eggs, applesauce, oil, and vanilla. In a separate bowl, mix flours, sugar, cinnamon, baking powder and soda, and salt.
Peel and grate carrots. Peel and dice apple. Add dry ingredients into the wet; mix until just combined. Fold in carrots, apples, raisins, walnuts and wheat germ.
Fill muffin cups 3/4 of the way full. Bake for 20-30 minutes or until a toothpick inserted comes out clean. Allow to cool in pan for 5 minutes; remove from pan and allow to cool to the touch.