Cut zucchini lengthwise in halves. Scoop out pulp, leaving 1/4-inch wall; chop pulp and reserve. Place zucchini shells cut sides down in dish. Cover loosely and microwave on high (100%) until crisp tender, about 5 to 6 minutes.
Cover and microwave reserved pulp, the onions and margarine in a 1 1/2-qt casserole or bowl on high (100%) until tender, 6 to 7 minutes. Stir in bread cubes, cheese, tomato, salt and pepper.
Turn zucchini shell cut sides up; spoon mixture into shells. Cover loosely and microwave on high (100%) until hot, 2 to 3 minutes.