Preheat oven to 325°.
To prepare custard layer, combine 1/4 cup sugar and 1/4 cup egg substitute, stirring well with a whisk. Cook the milk in a small, heavy saucepan over medium-high heat to 180° or until tiny bubbles form around edge (do not boil). Remove from heat; add semisweet chocolate, stirring until chocolate melts. Gradually add hot milk mixture to sugar mixture, stirring constantly with a whisk.
Pour the hot milk mixture into 6 (4-ounce) ramekins or custard cups coated with cooking spray. Place ramekins in a baking pan; add hot water to pan to a depth of 1 inch. Bake at 325° for 30 minutes or until almost set. Remove from oven; cool in pan 30 minutes. Remove ramekins from pan; drain water.
To prepare cake layer, place dark chocolate in a small glass bowl. Microwave at high 2 minutes or until almost melted; stir after 1 minute. Set aside. Beat 1/3 cup sugar and 1/3 cup egg substitute with a mixer at medium speed until well blended (about 5 minutes). Add dark chocolate and applesauce; beat until well blended. Pour evenly over the custard layer. Place ramekins in baking pan; add hot water to pan to a depth of 1 inch. Bake at 325° for 20 minutes. Remove ramekins from pan. Top each serving with 1 tablespoon whipped topping.