The key to remember is resistance without being restrictive. A high flow cat will add necessary resistance yet open up the flow a bit. It will add a nice 5-10 HP boost and add a more agressive sound.
Mandreal bends in your pipe is a nice expensive alternative that allows for nice out flow. A muffler option again adds performance due to internal design.
Any stock exhaust is WAY to restrictive, you'll notice a nice increase. The muffler should add another 10HP to the system. What you choose to do with the resonator, its up to you.
As for the intake, some gut, some go intake pipe and filter or rig up a true CAI intake system. Remember, do them at the same time, or do the exhaust first, doing an intake first and ignoring the exhaust is not going to help