I heard baking soda (sodium bicarbonate) and lemon juice on rust seems to break down the corrosion and make it removable. My results agree with that hypothesis. Not much more is required other than time and good old fashioned elbow grease. I've also added some water along the way since some people have said the lemon juice doesn't make that much of a difference.
These mufflers were from Magnaflow for the 2005 Pontiac GTO X-Pipe setup. They're 2.5" and I was upgrading to a custom 3". The whole setup ended up selling and I got a good price for it. So, for me, this was well worth the effort.