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Preheat oven to 400.
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Whisk together milk and flour in a medium saucepan and bring to a boil over high heat. Reduce heat, add nutmeg, and cook, stirring until thickened, about 10 minutes.
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Add cheddar, Gouda, Gruyere, cayenne, and pepper; whisk until melted, 1 minute. Add macaroni and stir to combine.
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Toss bread crumbs, Parmesan, thyme, parsley, oil, salt, and pepper in a small bowl.
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Place six individual crocks, ramekins, or ovenproof bowls on a rimmed baking sheet. Spoon 1 cup macaroni mixture into each ramekin and sprinkle with 1/6 cup bread-crumb topping.
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Bake until topping is browned and cheese is bubbling, 30-35 minutes. Serve hot.