Melt the stick of butter in a large pot over low/medium heat. Add the onions, garlic, bay leaves, thyme, and salt and pepper and cook until the onions are very soft and caramelized, about 30 minutes. Add the wine, bring to a boil, reduce the heat and simmer until the wine has evaporated, about 5 minutes. Discard the bay leaves and thyme sprigs. Dust the onions with the flour and give them a stir. Turn the heat down to medium low so the flour doesn't burn, and cook for 10 minutes. Add the beef stock (I prefer Better Than Bouillon) and Bouquet Garni, bring the soup back to a simmer, and cook for at least 30 minutes (I prefer to let it cook for up to 2 hours) Season, to taste, with salt and pepper.

Right before serving preheat the broiler and use broiler safe soup bowls. Place the bowls on a baking sheet fill with soup, then arrange the croutons on top of the soup in a single layer (about 1/2 cup per serving). Generously cover with the cheese and broil until bubbly and golden brown, 3 to 5 minutes. Serve with slices of toasted french baguette.

Alternative method: Ladle the soup into bowls, top each with 2 slices of bread and top with cheese. Put the bowls into the oven to toast the bread and melt the cheese. (I use croutons because I like the ability to fit on the spoon, plus it keeps the cheese on top better.)

This soup sometimes tastes better the next day, so feel free to make a day in advance and reheat before finishing in the broiler.