Preheat oven to 400°F. Cook macaroni in a pot of boiling salted water until slightly tender but still firm, 5 to 6 minutes. Drain, run under cold water, drain again.
In a medium saucepan, melt butter over low heat. Add flour and whisk for 3 minutes. Gradually whisk in milk, then mustard and 1/8 tsp. pepper until thoroughly combined.
Bring sauce to a simmer over medium-high heat and cook, stirring often, until slightly thickened, 10 to 15 minutes. Remove from heat and stir in cheese until melted. Season with salt and pepper. Pour sauce over macaroni and stir well. Divide mixture among 8 small ovenproof baking dishes; top with crushed saltines.
Bake until macaroni mixture is bubbling and cracker crumbs are golden brown, 10 to 15 minutes.