Preheat oven to 350°.
Spread zucchini on several layers of paper towels; sprinkle with 1/4 teaspoon salt. Cover with additional paper towels. Let stand 15 minutes, pressing occasionally until barely moist. Set aside.
Heat a saucepan coated with cooking spray over medium heat. Add shallots, and cook 5 minutes or until soft, stirring often. Remove pan from heat.
Lightly spoon flour into a dry measuring cup; level with a knife. Combine flour and 1/3 cup milk, stirring with a whisk. Add 1 cup milk; stir with a whisk. Add milk mixture to pan; cook 3 minutes over medium heat or until thick, stirring constantly.
Place milk mixture, 1/2 teaspoon salt, chopped basil, and next 6 ingredients (chopped basil through egg whites) in a food processor or blender; process until well blended. Add cheese, and process until well blended. Add zucchini, and pulse until combined.
Divide zucchini mixture evenly among 8 (4-ounce) ramekins or custard cups coated with cooking spray. Place ramekins on a jelly roll pan; add hot water to pan to a depth of 1 inch. Bake at 350° 30 minutes or until puffed and brown and a wooden pick inserted in center comes out clean. Remove ramekins from pan; run a knife around edges. Invert custards onto plates. Top with tomato; garnish with basil sprigs, if desired.