Take out pulp and seeds from the tomato halves and place in cheesecloth over a bowl. Squeeze to release juices. Throw away solids, saving 1/4 cup of liquid.
Arrange tomato halves, cut side up on an 11 by 17 inch baking sheet. Season with 1/4 teaspoon salt and pepper.
Put bread cubes in a large bowl and pour tomato liquid over top. Mix in 1/4 teaspoon salt, basil, olive oil, oregano, thyme, and garlic. Spoon bread mixture into tomato halves, lightly pushing down. Top each tomato with 1/2 teaspoon cheese. Bake for 12 minutes or until just heated through and tender.