1. Melt 2 tablespoons butter in a large skillet over moderate heat. Add onion, celery, and thyme; cook, stirring, until vegetables are softened, about 4 minutes. Add flour and cook, stirring constantly, until flour is golden, about 4 minutes. Add milk in a slow stream, whisking constantly, and cook until thickened and reduced to 1-1/2 cups, about 4 minutes. Remove pan from heat; whisk in cheeses and nutmeg. Salt and pepper to taste.
2. Bring a large pot of water to a boil; add salt. Stir in pasta and cook until al dente, about 7 minutes. Drain pasta and return to pot. Gently stir together pasta and cheese mixture; salt and pepper to taste. Spoon into eight 5- to 8-ounce ovenproof ceramic dishes.
3. Preheat oven to 350 degree F and arrange rack in middle of oven. Melt remaining 2 tablespoons butter in a nonstick skillet over moderate heat. Add bread crumbs and cook, stirring, until golden, about 3 minutes. Transfer to a bowl and stir in horseradish. Sprinkle tops of macaroni and cheese with crumb mixture. Bake on a cookie sheet until hot and crumbs are golden brown, about 20 minutes. Makes 8 servings.