Combine brown sugar, salt, and pepper. Set aside.
Place rice in bottom of a lightly greased 13- x 9- x 2-inch baking dish. Layer eggplant, onion, squash, zucchini, green pepper, and tomato in baking dish; sprinkle brown sugar mixture over each layer. Dot with butter. Cover tightly, and bake at 350° for 1 1/2 hours or until rice and vegetables are tender.