If you're wanting something that looks as well as sounds good, you'll want the Borla. If you're looking for just the sound, go with the Flowmaster since it's typically not as expensive. From the sound clips I've heard, I'd say they sound about the same. The main difference being that the Flowmaster is just a muffler, the Borla is the whole rear portion of the exhaust system so you get a nice shiny new tip as well. Well, that an about $200 more for the Borla.
Borla is very good and you can do it yourself. A flowmaster you would probaly have to take it to a shop and have it spiced in to fit and welded and that will cost money as well.
03, Abyss monotone GT, 6 disk changer, moon and tunes, Cargo mat/nets, power package, side airbags, AEM Short Ram Intake, Borla exhaust , 35% tint all around, F1 strut tower brace, debadged, 17" Excel rims w/ federal ss595 tires.