Lay flounder on a cutting board, light side down; slit lengthwise, beginning 3/4 inch from head and cutting down center of fish to tail. Make a crosswise slit in flounder near head. Cut flesh along both sides of backbone to tail, allowing the knife to run over the rib bones to form a pocket for stuffing. Set fish aside.
Combine next 5 ingredients in a small mixing bowl, tossing lightly to mix. Spoon mixture into pocket of fish. Top fish with onion and lemon slices. Place bacon over fish across pocket opening. Dot with butter.
Bake, uncovered, at 350° for 30 minutes or until fish flakes easily when tested with a fork. Remove onion, lemon slices, and bacon, and discard. Transfer to a serving platter. Sprinkle with salt and pepper. Garnish with lemon halves and parsley sprigs. Serve immediately.