Preheat oven to 400 degrees F (200 degrees C). Lightly grease 24 muffin cups.
In a bowl, sift together the all-purpose flour, whole wheat flour, oat flour, salt, baking powder, baking soda, cinnamon, and nutmeg. In a separate bowl, beat together eggs, vegetable oil, applesauce, yogurt, sugar, honey, and vanilla. Mix the flour mixture into the egg mixture. Fold in the zucchini, carrots, pecans, and raisins. Scoop into the prepared muffin cups.
Bake 18 to 20 minutes in the preheated oven, until a toothpick inserted in the center of a muffin comes out clean. Cool 10 minutes before transferring to wire racks to cool completely.