In a 10- to 12-inch frying pan over medium-high heat, frequently stir onions and 1 tablespoon olive oil until onions begin to brown, 12 to 15 minutes. Season to taste with salt and pepper.
Meanwhile, rinse tomatoes, core, cut in half, and squeeze out seeds. Thinly slice tomatoes crosswise.
Combine basil, thyme, and garlic. Mix 1/2 of the herbs with zucchini.
Spread cooked onions in a shallow 2- to 3-quart casserole. Distribute zucchini evenly over onions.
Layer tomato slices over sliced zucchini. Sprinkle evenly with remaining herb mixture and lightly with salt and pepper. Drizzle vegetables with remaining olive oil.
Bake in a 400° oven until tomatoes are browned and zucchini slices are tender when pierced, 35 to 40 minutes (30 to 35 minutes in a convection oven). Add salt and pepper to taste.