Trim Brussels sprouts; cut X in base of each. In saucepan of boiling salted water, cook Brussels sprouts for 7 to 9 minutes or until tender-crisp. Drain and chill under cold running water; press out excess water with towel. Cut in half if large; place in shallow greased 8-cup (2 L) casserole dish.
In saucepan, melt butter over medium heat; cook onion and thyme, stirring occasionally, for 5 minutes or until softened. Sprinkle with flour; cook, stirring, for 1 minute. Add milk; cook, stirring, for 6 to 8 minutes or until thickened. Remove from heat and stir in cheese, salt and pepper; pour over Brussels sprouts.
Topping: In bowl, stir together bread crumbs, cheese and butter. (Make-ahead: Cover Brussels sprouts and topping; refrigerate for up to 1 day.).
Cover and bake Brussels sprouts in 375°F (190°C) oven for 30 minutes. Uncover and sprinkle with topping; bake for about 20 minutes or until golden and bubbly.