This bistro classic is deceptively easy to make. It just takes a little time and a few good ingredients. We found that yellow onions, also known as Spanish onions, work best for this recipe. They have a nice balance of sweetness and bitterness and caramelize perfectly. Just don't take them too dark -- a nice golden brown is perfect. Good beef broth also makes a big difference. If you can't make your own, look for a high-quality prepared variety.
Melt the butter in a very large Dutch oven or pot over medium heat. Add the onions, bay leaves, thyme, 1 teaspoon salt, and a few grinds black pepper. Cook, stirring occasionally, until the onions are very soft and light golden-brown, about 1 hour. (The onions will begin to stick to the bottom of the pan and turn brown after about 30 minutes; just keep scraping them up and stirring them into the rest of the onions. If they are browning to quickly, lower the heat.)
Add the wine to the pot, bring to a simmer and cook until it has almost completely evaporated, about 4 minutes. Add the beef broth and 1 cup of water, bring to a simmer and cook until the flavors come together and the soup is rich, about 45 minutes. Remove the bay leaves. Season with 1/2 teaspoon salt and a few grinds of black pepper. Keep the soup warm on a low burner or cool completely and refrigerate to reheat later. (The soup can be refrigerated for up to 2 days or frozen for up to 1 month.)
Preheat the broiler. Place four soup crocks on a rimmed baking sheet and fill them about 3/4 of the way with hot soup. Float a slice of baguette on top of each and cover with 1/2 cup Gruyere. Broil until the Gruyere is golden brown (don't be alarmed if some soup bubbles out), 2 to 3 minutes.
Slice the onions from stem to root. This allows them to retain more of their shape during cooking than when sliced crosswise.
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