Melt the butter in a large soup pot over medium-high heat. Add the shallots, onions, garlic and honey. Cook about 10-15 minutes, stirring frequently, until softened, deep golden in color and caramelized. Add the thyme and sage and continue cooking another 3-5 minutes.
Reduce the heat to low and sprinkle the flour over the shallots, stirring for 1-2 minutes, until the raw flour taste is eliminated. Add the wine, broth, Worcestershire sauce, and bay leaves. Increase the heat to medium-high and return the soup to a simmer, simmer for 10 minutes. Remove the bay leaves and discard. Season, to taste with salt and pepper.
Preheat the broiler to high.
Ladle the soup into oven safe bowls. Add a slice of bread to each and top evenly with each cheese. Place each soup bowl on a baking sheet and transfer to the oven, broil until bubbly and golden brown, 3 to 5 minutes.