Combine sugar and water in a 2 quart saucepan set over medium heat. Without stirring, cook mixture until dark amber in color, swirling the pan carefully while cooking, about 20 minutes. Reduce the heat to low. Slowly add cream, stirring with a wooden spoon. Scrape the vanilla seeds into the pan and add the pod. Add lemon juice, butter and bourbon. Stir to combine. Cover and refrigerate up to one week. Bring sauce to room temperature or warm over low heat before using.
Heat oven to 325 degrees. Place apples in a small bowl, and toss with lemon juice; set aside. Butter six 8 oz ramekins or custard cups; place in roasting pan. Cut brioche into eight slices, then quarter each slice; set brioche aside. In a large bowl, whisk together cream, eggs, sugar, salt, vanilla and nutmeg. Add brioche and toss to coat. Place 1T. of the caramel sauce into each ramekin. Add approximately 1/3 C apple mixture, then 1/3 C bread mixture. Add a second layer of sauce, apples and bread. Carefully place the roasting pan on the center oven rack. Fill roasting pan with hot water to within 1/2 inch of ramekin tops. Cover pan with aluminum foil. Cook 20 minutes. Remove foil; cook for 20 minutes more. Remove roasting pan from the oven and transfer the ramekins to a wire rack to cool for 5 minutes. Using a towel, invert ramekins onto a serving platter. Serve warm with remaining caramel sauce on the side.