My personal preference is Magnaflow. I have them on my FJ, and my 2500HD, and will put them on my square as well.
My reason for it isn't sound, I generally go quiet when the choice is there. The reason is quality. If you hold a Magnaflow and a Flowmaster in your hand, it's immediately obvious which one is the better muffler. I could beat someone to death with a Magnaflow and it would still be whole, the Flowmaster would just piss them off and split lol.
My Flowmasters generally rotted out in 2-3 years on daily driven vehicles.