Preheat the oven to 325°F. Combine the tomatoes, mini peppers, and shallots in a 13×9-inch glass baking dish. Pour ½ cup oil over. Mix in 3 tablespoons of the vinegar, marjoram, salt, red pepper flakes, and black pepper. Place in the oven and roast until the tomatoes collapse and flavors are rich, stirring once or twice, about 1 hour.