Preheat oven to 350°F. In skillet, fry bacon until crisp; set aside to cool. Reserve 1 tablespoon bacon grease in pan for sautéing onion; sauté onion until edges turn brown, about 5 minutes.
To make breadcrumbs, melt 2 tablespoons butter in skillet and add rye bread. Stir over medium heat until browned, about 10 minutes. Remove from heat and set aside.
Cook pasta according to package directions until al dente. In separate saucepan, melt remaining 3 tablespoons butter; add flour. Whisk on medium heat about 1 minute to form rough paste.
Slowly add warm milk, whisking constantly over medium heat, 10-15 minutes, or until sauce thickens. Remove sauce from heat and stir in brown mustard, limburger, salt and pepper.
In large mixing bowl, combine bacon, onion, macaroni and cheese sauce. Stir well, then ladle into 6 individual-size, oven-proof bowls or 2-quart baking dish. Top with parmesan cheese and rye bread crumbs. Bake 30 minutes.
Serve Limburger Helper with a crisp wheat beer and pickles.