Cut each squash crosswise into 4 (1-inch) rings; discard seeds and end pieces. Set squash aside.
Combine onion, oil, and orange rind in a 13 x 9-inch baking dish; toss well. Bake at 400° for 15 minutes or until onion is golden. Discard orange rind. Arrange squash in dish, slightly overlapping the rings. Combine basil, pepper, garlic, and tomatoes; spoon over squash rings. Cover and bake at 400° for 30 minutes or until squash is tender. Top with cheese; bake, uncovered, an additional 5 minutes or until cheese melts. Garnish with basil sprigs, if desired.