Preheat oven to 425 degrees F. Coat twenty-four 1-3/4-inch muffin cups with cooking spray; set aside. For pastry, in a large bowl stir together flour, Parmesan cheese, and salt. Add oil all at once. Mix until crumbly. Add 2 tablespoons of the ice-cold water; stir to combine. Add enough remaining water, 1 tablespoon at a time, until flour is moistened. Gather into a ball, then knead gently just until pastry holds together.
Divide pastry in 24 portions. Press each portion into a muffin cup. Do not prick pastry in cups. Bake for 8 to 10 minutes, just until pastry begins to brown. Remove from oven; set aside. Reduce oven to 350 degrees F.
For quiche filling, in a small bowl whisk together egg, milk, and pepper. Stir in the cheese and onion. Fill each pastry cup with about 1 teaspoon filling. Top each quiche with a tomato slice or herb leaves.
Bake quiches for 20 minutes or until filling is puffed and set. Cool in muffin cups on a wire rack for 5 minutes. Remove from cups; serve warm. If desired, sprinkle with fresh thyme.