These incredible brownies are filled with a layer of gooey salted caramel which can be made two weeks in advance. Slideshow: More Brownie Recipes
In a medium saucepan, cook the sugar with the water over moderate heat, swirling the pan frequently, until a dark amber caramel forms. Slowly drizzle in the cream, then whisk in the butter and sea salt. Transfer the caramel to a small bowl and refrigerate until thickened, about 2 hours.
Preheat the oven to 325°. Lightly butter a 9-by-13-inch metal baking pan. Melt the 2 sticks of butter in a heatproof medium bowl set over (not in) a saucepan of simmering water. Add the chopped chocolate, the sugar, cocoa powder, vanilla and salt and stir until smooth. Remove the bowl from the heat and whisk in the eggs. Add the flour and stir until just incorporated. Scrape the batter into the prepared pan and bake the brownies for about 40 minutes, until a tester inserted in the center comes out with a few moist crumbs attached. Transfer the pan to a rack and let cool completely.
Invert the brownies onto a cutting board and cut in half to form 2 rectangles. Spread the chilled caramel over 1 rectangle, then top with the other rectangle. Cut into 12 bars and serve immediately.
The caramel can be refrigerated for 2 weeks. The brownies can be refrigerated for 3 days or frozen for 1 month.