My 2006 Mustang makes a weird noise at a stop

Try to isolate where the knocking is coming from - you don't specify an engine knock, so we'll have to make that assumption. An engine knock that goes away under higher RPMs or load tend to be related to an oil bearing, rod, or wrist pin. Upper valve train noises tend to be 'ticks' rather than knocks. Take it to someone with a trained ear for engine knocks, and be prepared for the worst sort of news (engine rebuild).