Heat the oil in a heavy large saucepan over medium-low heat. Add the onions, carrots, fennel, and bay leaves and sauté until the onions begin to brown (caramelize), about 20 minutes.
Add the tomatoes, 5 cups of broth, lentils, and 1 tablespoon thyme. Bring to a boil, reduce the heat and simmer until the lentils are tender, stirring occasionally and thinning with more broth as needed, 30-45 minutes.
Meanwhile, prepare the quinoa (see recipe below).
Season the lentil ragout to taste with salt and pepper. Add the chard and simmer until wilted, about 5 minutes. Add more broth to thin to a thick ragout if needed. Cover to keep warm.
Prepare the eggs: For 4-6 eggs use 1 skillet, for more eggs use 2 skillets. Fill 1 or 2 large, deep skillets ¾ full with salted water and bring to a boil. Add 1 tablespoon vinegar to each skillet. Break an egg into a cup, and then slide the egg into the water. Repeat to add the remaining eggs to the skillet. Bring the water back to a simmer and cook gently until the whites are set, about 2 minutes.
Divide the quinoa among 6 plates. Top each with some lentil ragout. Using a slotted spoon, transfer 1 or 2 eggs to each plate. Top with yogurt if desired and sprinkle with additional thyme and serve right away.