Lightly coat 2 cookie sheets with nonstick cooking spray; set aside. In a large bowl, stir together the apple, peanut butter, egg, brown sugar canola oil, and vanilla. In a small bowl, combine the flours, wheat germ, cinnamon and baking soda.
Stir flour mixture into peanut butter mixture, stirring until combined. Stir in peanuts. Drop dough by slightly rounded tablespoons 2 inches apart on prepared cookie sheets. Flatten slightly.
Bake in a 350 degree F oven for 9 to 10 minutes or until cookies are lightly browned on bottoms. Transfer to wire racks to cool completely. Makes about 20 cookies.