In a large soup pot or Dutch oven, melt the butter over medium heat. Add the onions, stir to combine with the butter, cover, and cook for 30 minutes, stirring occasionally. Remove the cover; increase the heat to medium-high and cook, until the onions are brown and caramelized, about 30 minutes. (Stir the onions frequently toward the end of this stage in the cooking, so they do not scorch or burn.) Add the thyme and garlic, saute for 2 to 3 minutes more. Pour in the wine and scrape up the browned bits from the bottom of the pan with a wooden spoon; simmer until the wine is reduced by about half. Stir in the broth and salt and bring to a gentle simmer. Cover, and cook for 30 minutes. Add the Cognac, if using, and season with pepper to taste. (The soup can be made to this point a day ahead and refrigerated.)

When ready to serve pre-heat the broiler. Heat the soup and divide it evenly among 6 heatproof crocks or bowls. Top each soup with a slice of the bread and about 1/2 cup of the cheese. Place the bowls on a sheet pan and broil until the cheese is bubbly and brown. Carefully transfer each crock to an under-lining plate. Serve immediately.