I have the 3 valve 4.6 in my Mustang GT and they have tuned the exhaust so that it sounds very good. Switching to the Shelby GT rear mufflers would make it sound a little more aggressive, and I can also get an X pipe from Ford or other companies.
This vintage of Mustang 4.6 (2005-20010) is very easy for relatively painless upgrades, since both Ford and aftermarket have a lot available. For example, the stock engine is 300 HP, but I could pick up 25 HP in an hour by just getting a CAI and tune from Ford Racing or another company. Ford even makes two levels of supercharger kits that you can get installed by a Ford dealer or do it yourself. If you want to stay with NA you can get also cam kits and intakes from Ford. The Ford parts are a little more conservative than aftermarket, but I think they are better engineered and require less tweaking to make them work right.