2 Tbs. olive oil
2.) Heat the oven to 375°F. Put the tomato slices on a shallow plate to drain for a few minutes and then discard the collected juices. In a medium bowl, toss the zucchini and squash slices with 1-1/2 Tbs. of the olive oil, the thyme, and 1/2 tsp. of the salt. Starting at one end of the baking dish, lay a row of slightly overlapping tomato slices across the width of the dish. Next, lay a row of zucchini, overlapping the tomatoes by two-thirds, and sprinkle with cheese. Repeat with a row of squash, and then repeat rows, until the gratin is full.
Season lightly with pepper and the remaining 1/2 tsp. salt. Drizzle the remaining 1-1/2 Tbs. olive oil over all. Combine the cheese with the remaining 1 Tbs. thyme and the cracker crumbs. Sprinkle this over the whole gratin. Cook until well-browned all over and the juices have bubbled for a while and reduced considerably, 65 to 70 minutes. Let cool for at least 15 min. before serving.