Heat one tablespoon of the olive oil in a large, oven-proof skillet over medium heat. Add the onion and bell peppers and saute until they're soft. Add the garlic and saute until it's fragrant.
Add in the crushed tomatoes, basil, and salt and pepper, and cook for a couple minutes.
Arrange the eggplant, squash, zucchini and tomatoes in a spiral in the skillet, starting around the outside edge and working your way in. (Stand the slices up on their ends, rather than laying them flat, and arrange them tightly.)
Mix the remaining olive oil with the rosemary and thyme in a small bowl, and spoon or brush the mixture as evenly as possible over the top of the vegetables. Top with more salt and pepper.
Cover the pan with aluminum foil and bake for one hour.
Serve alone, with pasta or as a side dish and sprinkle servings with grated parmesan.