In a large Dutch oven or heavy pot over medium heat, melt butter. Add the onions, half of the thyme leaves, salt and pepper and cook, stirring occasionally, until onions are soft and caramelized, about 15-20 minutes.
Stir in the flour until completely combined, then turn the heat up to medium high and deglaze the pan with the sherry. Simmer until the sherry is reduced to about 1/4 cup, 2-3 minutes, then stir in the beef broth. Bring the broth to a simmer, then stir in the elbow macaroni. Cook according to package directions for al dente, about 5-6 minutes.
When macaroni is cooked, stir in 1 1/2 cups gruyere cheese, 1 cup Colby jack cheese and 1 cup mozzarella cheese. Fold the cheeses into the pasta to melt, then add remaining thyme, sage, chopped parsley, salt and pepper.
Divide the mac and cheese into 6-8 ounce crocks. Top each with 1/4 cup toasted panko and remaining 1 cup gruyere, 1 cup Colby Jack and 1 cup mozzarella.
Preheat oven to broil. Place the crocks on a baking sheet and brown the Mac and Cheese until the cheese is melted and the browning in spots, about 3-4 minutes.