Preheat oven to 375 degrees F. Line a muffin tin with paper cups or grease lightly, and set aside.
In a large mixing bowl, cream together cream cheese, butter, and sugar until light and fluffy. Add eggs, lemon juice, and vanilla extract and mix well. Add milk and mix until combined. Mix in flours, bran, germ, baking powder, baking soda, and salt just until blended. Stir in apples by hand.
Fill prepared muffin tin with batter, 2/3 to 3/4 the way full. Bake in preheated 375 degree F oven for 18 to 23 minutes, or until a toothpick inserted near the center of a muffin comes out clean. Let cool on wire racks before storing at room temperature in an airtight container.