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.