Traditionally the big-name exhaust systems are incredibly good quality and are generally made from much better materials (eg. stainless or titanium piping).
In addition to this, the big-name systems tend to have well constructed mufflers which often flow incredibly well, compared to some of the cheap generic mufflers you sometimes come by.
You get what you pay for... but shagged if I'm paying three times the price for something that is maybe 10% better. I'll never go anywhere but a custom exhaust shop.