Position an oven rack in the center of the oven and preheat it to 400 degrees F. Lightly grease a 3-quart baking dish with butter and set aside.
Fill a small pot with lightly salted water and bring to a boil over medium-high heat. Add the barley and boil until just cooked through but still slightly chewy, about 20 minutes (it will continue to cook in the oven). Drain and rinse.
Meanwhile, put 2 tablespoons of butter in a medium microwave-safe bowl and microwave until melted, about 30 seconds. Combine the Gruyere, mozzarella and Parmesan in another medium bowl. Add the panko, 1 cup of the cheese mixture and 1/2 teaspoon salt to the bowl with the melted butter. Use your hands to work the butter into the cheese and breadcrumbs. Set aside.
Melt the remaining 6 tablespoons of butter in a wide large pot over medium-high heat. Add the onions and a large pinch of salt and cook, stirring occasionally, until the onions are lightly browned, 6 to 8 minutes. (The butter will start to foam and brown specks will form, but that is okay; this will add a lot of flavor to the finished dish.) Reduce the heat to medium, add the garlic and thyme and stir constantly until the garlic is just softened, about 1 minute. Stir in the flour and cook, stirring constantly, until a thin paste forms around the onion mixture, about 1 minute. Whisk in the milk and 1 teaspoon each salt and pepper and bring to a boil over medium-high heat. Reduce to a simmer, stirring occasionally until the sauce is a thin gravy, about 10 minutes. Remove from the heat and stir in the shredded cheese mixture and cooked barley. Season to taste with additional salt and pepper. Spoon into the greased baking dish. Sprinkle the reserved cheesy breadcrumbs evenly on top of the barley and bake until bubbly and the top is golden brown, about 30 minutes. Let stand 10 minutes before serving.
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From Food Network Kitchen