Peel eggplant and cut into circular slices 3/8-inch thick. Place eggplant in colander and toss with salt. Let stand 30-45 minutes. Drain. Dry each slice in a towel.
Scrub zucchini & squash, slice off two ends, and cut into slices about same size as eggplant. Toss with olive oil, salt & pepper and place on baking sheet. Roast zucchini & squash for 10-12 minutes. Set aside.
Meanwhile, saute eggplant in olive oil for about 2 minutes on each side to brown lightly; do not overcrowd. Remove to a side dish with towel to drain excess oil.
In same skillet, cook onions in olive oil for about 5-7 minutes, or until tender but not browned. Stir in garlic and continue to sauté careful not to brown. Season with salt, pepper, thyme, coriander and fennel seed. Add crushed tomatoes.
Place 1/3 tomato sauce in bottom of covered casserole (min. 2 1/2 inches deep) and sprinkle ½ of the basil. Arrange in layers the eggplant, then zucchini & squash, then add another 1/3 tomato sauce. Layer remaining eggplant, zucchini & squash on top and finish with remaining tomato sauce and basil.
Cover casserole and simmer on very low heat for 10 minutes. Uncover, tip casserole and baste with accumulated juices. Correct seasoning, if necessary.
Cook uncovered 15 minutes, basting several times, until juices have evaporated leaving a spoonful or two of flavored olive oil.
Set aside uncovered. Reheat slowly at serving time, or serve cold.