Combine bran Flakes, raisins and milk in large mixing bowl. Stir together whole wheat flour, soy flour, wheat germ, baking powder, nutmeg and salt; set aside.
Combine eggs, honey, oil and molasses in small bowl; blend well. Add egg mixture to soaked bran flakes; mix well. Add dry ingredients all at once to bran mixture, stirring just enough to moisten. Spoon batter into paper-lined 3-inch muffin-pan cups, filling 2/3rds full.
Bake in 350 degrees F oven 25 minutes or until golden brown. Serve hot with butter and homemade jelly or jam.