Combine shallots, 2 onion quarters, ginger, and garlic in a food processor; pulse into a paste.
Heat oil in a large pot over medium-high heat; cook and stir cloves, nutmeg, and cinnamon until fragrant, about 30 seconds. Add shallot paste and fry until fragrant and slightly browned, 2 to 3 minutes. Add oxtails; stir until completely covered with spices and paste and browned, about 5 minutes.
Stir remaining onion quarters, 2 carrots, and celery into the pot. Pour in enough water to cover by 2 inches. Bring to a boil; reduce heat, cover, and simmer until oxtail is tender, about 5 hours.
Stir salt, black pepper, potatoes, and 3 carrots into the pot. Increase heat and simmer soup until potatoes and carrots are tender, about 15 minutes. Add sugar and fish sauce; stir well to combine.
Ladle soup into large serving bowls and top with tomato wedges and French-fried onions.
