In a medium saucepan, melt butter over medium-high heat; add onions. Cook, stirring, for 5 minutes. Reduce heat to medium-low and continue cooking, stirring often, until very soft and golden brown, about 20 minutes.
Increase heat to medium-high; stir in leeks, mushrooms, garlic and thyme. Cook, stirring occasionally, until mushrooms are softened and most of the liquid has evaporated, about 10 minutes. Stir in flour; cook, stirring, for 1 minute.
Stir in wine; cook, stirring, for 30 seconds. Stir in broth and 2 cups (500 mL) water; bring to a boil. Reduce heat and simmer for 10 minutes, stirring occasionally. Stir in salt and pepper.
Position upper oven rack about 8 inches (20 cm) from heat. Preheat broiler. Ladle soup into 4 ovenproof soup bowls; place on a baking sheet. Top each bowl with 2 slices toasted baguette; sprinkle with cheese and top with chives. Broil, watching closely, until cheese is bubbly and golden, 2 to 3 minutes. Garnish with small sprigs of thyme, if desired.
Per Serving: 333 calories, 13 g protein, 14 g fat (8 g saturated fat), 37 g carbohydrates, 3 g fibre, 40 mg cholesterol, 705 mg sodium