Mix all cheeses. Set aside 1 cup for topping; cover and chill.
Melt 4 tablespoons butter in large saucepan over medium heat. Add flour and stir until mixture turns golden brown, about 4 minutes. Add thyme and nutmeg. Gradually whisk in milk. Simmer until thickened and smooth, stirring often, about 4 minutes. Add cheeses from large bowl. Stir until melted and smooth.
Melt 1 tablespoons butter in heavy large skillet over medium-high heat. Add breadcrumbs,; toss. Stir until golden, about 2 minutes. Transfer to plate.
Preheat over to 375 degrees. Cook pasta in boiling salted water until tender but firm to bite. Drain. Transfer to large bowl. Pour cheese sauce over; toss. Divide among 8 1 1/4 cup custard cups. Sprinkle with 1 cup reserved cheese. Place cups on rimmed baking sheet.
(Can be made 1 day ahead. Cover with foil; chill. Drizzle each with 1 tsp cream. Cover with foil; bake 15 minutes. Uncover and proceed).
Sprinkle partially baked, chilled, or just assembled cups with bread crumbs. Bake pasta until beginning to bubble and tops are golden, about 20 minutes.