Heat oil in a medium skillet, over medium heat. Add the onion slices and sauté until lightly browned.
Lightly grease or spray a casserole dish. Arrange the caramelized onions on the bottom and layer the potato, tomato and squash, edges overlapping, on top. Season with salt and pepper, sprinkle with thyme and Parmesan and drizzle with olive oil.
Cover the dish with foil and bake for 30 minutes. Remove the foil and bake another 20-30 minutes or until the potato is tender.
Inspired by a September 2011 Wholeliving.com recipe