Preheat oven to 375 degrees F. Grease twelve 2 1/2-inch muffin cups; set aside. In a small skillet or saucepan heat olive oil over medium-high heat. Add shallots; cook 3 minutes or until just tender. Remove from heat; let cool.
In a large bowl whisk egg whites to soft peaks. In a second large bowl whisk together egg yolks, milk, and crushed red pepper. Stir in cooked shallots, cheeses, and parsley. Gently fold egg whites into the yolk mixture.
Spoon 1/4 cup egg mixture into each prepared muffin cup. (Cups will be nearly full.) Top each with a few tomato slices and additional parsley. Bake 18 to 20 minutes or until puffed, set, and golden brown. Let cool 5 minutes on a wire rack. (Egg bakes will fall as they cool.) Loosen sides; remove from cups. Serve warm or at room temperature (can sit up to 2 hours). Reheat in a 325 degrees F oven for 12 to 15 minutes.