1. Melt 1 tablespoon butter in heavy large pot over high heat. Add onions and thyme; saute until onions begin to soften. Reduce heat to low; cook until onions are caramelized, stirring occasionally, about 20 minutes. Transfer onion mixture to medium bowl. 2. Melt remaining 2 tablespoons butter in same pot over medium-high heat. Add mushrooms; saute until soft, about 12 minutes. Add cognac or brandy and garlic; stir 20 seconds. Stir in onion mixture, then veggie broth and wine. Bring to a boil. Reduce heat to low; simmer until onions are very tender, about 45 minutes. Discard thyme sprigs, season with salt and pepper. 3. Preheat broiler. Place baquette slices on large baking sheet. Spread with soy cheese and broil until brown spots begin to appear on cheese, watching carefully so they don't burn. 4. Serve soup, floating croutons on top of each bowl.