Preheat the oven to 375 degrees F.
In a medium saute pan, heat the olive oil to medium heat. Place the onions in the pan and over low heat, slowly cook the onions. Cook until onions are soft and sweet, approximately 15 minutes. When done, season the onions with sugar, vinegar, and salt to taste. Remove the onions from the pan and set aside to cool.
Cook's Note: The onions can be made up to 2 days ahead of time and reserved in the refrigerator.
Have cheeses at room temperature. Put the goat cheese, Cheddar cheese, and Gruyere cheese in a bowl and mix together well. Season the cheeses with the truffle oil.
Assemble the sandwiches by placing half of the cheese mix on 1 slice of bread, 1/2 of the onions on a second slice and top with 1/2 the toasted pine nuts. Join the two pieces of bread and repeat the process for the second sandwich.
In a large saute pan, (large enough for two sandwiches) place the clarified butter and bring to medium heat. Carefully place the sandwiches in the pan and toast each side for approximately 2 minutes each. Remove the pan from the stove and place in oven to heat through to the center of the sandwich, about 3 minutes. Carefully, remove the pan from the oven and serve the hot sandwiches.