I have Flowmaster 50 Series on mine, which not a lot of people do. I enjoy them because they aren't too loud during everyday driving and on the highway, just a nice rumble that lets people know that it isn't stock. When you get into the higher RPM's however it gets aggresive and very complete sounding unlike the raw sound of the 40's and 44's.
The 40's ad 44's are great for attention grabbing and they do just that. That classic sound is awesome.
I also have the pypes high flow cats on my setup and they work fine. The SES light came on a couple times because of a few leaks but with an OBDII scaner you can delete the code after the leaks are taken care of.
K&N CAI, Pypes X Mid Pipe w/ High Flow Cats, Flowmaster Catback Exhaust w/ 50 series mufflers, Steeda Tri-Ax Short Throw Shifter,