In a medium saucepan, melt the 3 tablespoons butter over low heat. Add the onions and sauté for 5 to 7 minutes, or until lightly golden and soft. Add the pancetta and sautè for 10 to 12 minutes, or until lightly browned. Remove from the heat and set aside.

Preheat the oven to 375°F. Butter two 3-quart baking dishes.

In a large saucepan, melt the 1/2 cup butter over medium-low heat. Add the flour and stir constantly for 3 minutes; do not browd. Whisk in the half-and-half and cook, whisking occasionally, until thickened, about 5 minutes. Remove from the heat, stir in the salt, pepper, and the 4 cups Parmesan cheese until the cheese is melted.

In a large pot of salted boiling water, cook the penne until tender but firm, about 12 minutes. Drain and toss with the cheese sauce. Add the pancetta mixture and toss thoroughly. Set aside.

In a medium bowl, combine the Gruyère and fontina. Stir to blend.

In a small bowl, combine the 3 tablespoons Parmesan cheese, the bread crumbs, and parsley.

Layer one-fourth of the pasta in each baking dish. Sprinkle each layer evenly with one-fourth of the cheese mixture. Repeat the process with the remaining pasta and cheese mixture. Cover the top with the bread crumb mixture.

Bake for 35 to 45 minutes, or until golden brown. Remove from the oven and let rest for 5 minutes before serving. If you are planning on reheating, bake the pasta for 25 to 30 minutes initially, then reheat for 10 to 15 minutes.