Preheat oven to 350 and lightly grease a 12-cup muffin pan.
Combine all ingredients for meatballs in a bowl. Mix very well until all ingredients are incorporated. Set aside.
Heat up oil in a cooking pan, over medium heat. Add sliced onions and sugar to the pan and saute until transparent stirring occasionally.
Stir in minced garlic, red wine and tomato paste, saute for a couple of minutes.
Sprinkle the mixture with flour and mix well.
Slowly add beef stock, while stirring the whole time.
Add salt and thyme and simmer for 5-7 more minutes.
Scoop about a tablespoon of French onion sauce (with some onions) in each muffin cup.
Scoop about 1/3 cup of meatball mixture and roll it into a big ball. Place meatball in the muffin cup, it should fit snugly. Repeat with remaining meat mixture.
Bake for 25-30 minutes.
Top off with remaining French Onion sauce, dividing it equally among the muffin cups.