Heat oil in large skillet set over medium heat; cook zucchini, red pepper, onion, garlic and half of the salt for about 5 minutes or until vegetables are softened. Let cool to room temperature.
Preheat oven to 375°F (190°C). Grease eight 1/2-cup (125 mL) ramekins. Whisk together eggs, milk, mustard, thyme, remaining salt and pepper until blended; fold in zucchini mixture and divide evenly among ramekins.
Sprinkle with goat cheese and top with halved cherry tomatoes. Bake for 22 to 25 minutes or until eggs are set. Serve warm or at room temperature.