Preheat oven to 350°F. Spray a 12-cup muffin pan with cooking spray or line with paper liners.
Topping: In a small bowl, mix brown sugar, flour, oats and salt. Work in butter with fingertips until mixture is crumbly. Set aside.
Muffins: In a large bowl, whisk together the all-purpose flour, whole-wheat flour, oats, brown sugar, wheat germ, cinnamon, baking powder, baking soda, nutmeg and salt until evenly combined.
In a medium bowl, whisk together yogurt, oil, egg and vanilla. Stir into flour mixture, just until combined. Fold in apples. Divide among muffin cups. Sprinkle with topping.
Bake until golden brown and a cake tester comes out clean, about 25 minutes. Let cool in pan on rack for 5 minutes; turn out onto rack. Let cool completely.