Cut an inch off the top and a little bit of the bottom of the tomatoes, so they stand upright. With a small spoon or melon baller, gently scoop out the inside of the tomatoes. Place the tomatoes in a shallow baking dish, and sprinkle with salt and pepper.
In a bowl, combine the bread crumbs, basil, parsley, garlic, thyme, and 1/2 teaspoon salt. Fill the tomatoes to the top with the bread crumb mixture. Drizzle a little olive oil over each.
Bake the tomatoes for 10-15 minutes, or until tender. Remove from oven and top with grated cheese.