Preheat the oven to 375°F. Lightly grease a large baking dish with a little olive oil.
In a mixing bowl, toss the eggplant, zucchini, bell peppers, onion, and garlic with 2 tablespoons olive oil, thyme, salt, and pepper until evenly coated.
Spread the chopped tomatoes across the bottom of the baking dish to create a base layer.
Arrange the seasoned vegetables in overlapping rows on top of the tomatoes. Drizzle the remaining tablespoon of olive oil over everything.
Bake uncovered for 35 to 40 minutes until the vegetables are soft and starting to brown at the edges.
While the ratatouille bakes, stir the goat cheese together with the basil and parsley in a small bowl.
Remove the dish from the oven and dot the herbed goat cheese across the top. Return to the oven for 5 more minutes until the cheese softens and warms through.