Heat oven to 350°F. Spray 1- to 1 1/2-quart casserole with cooking spray. In 2-quart saucepan, melt butter over medium heat. Add onions; cook and stir 2 to 3 minutes or until tender.
Stir in flour, salt and pepper. Gradually add milk, stirring constantly. Cook and stir until mixture is bubbly and thickened. Remove from heat.
Add 3/4 cup of the cheese; stir until melted. Stir in cooked vegetables. Spoon mixture into casserole. Sprinkle with crushed crackers and remaining 1/4 cup cheese.
Bake 25 to 30 minutes or until topping is golden brown and casserole is bubbly.