Mufflers: Well...I'm gonna go ahead and be the first to vouch for 40 Flows. Yes half the musclecars and muscletrucks on the road have em, but in my opinion they simply can't be beat. I lucked out in the fact that somehow there's only one other person in town with em (loud ones atleast). They sound awesome, deep, rumbly and metallic at idle and scream at WOT.
Headers: If you're doing full exhaust I'd definately recommend headers too. Different headers will give you a different sound, hopefully someone will chime in on exactly what they are... longtubes cut down on drone and produce a quieter idle and louder WOT i believe.
Pipes: Based on your engine performance, the wilder, more powerful the engine the bigger the pipe... (anywhere from 2-3" as far as I've heard). Smaller pipes give more torque and backpressure and bigger pipes let the air flow better at high rpm. Smaller pipes also tend to sound more crisp while largers are louder and hollower.
Crossover Pipe: H for chambered mufflers, X for straight thrus. H for more of the musclecar sound, X for the Euro sports car sound.
Tips: Turndowns are louder and "mushier", tailpipes are crisper.
Keep in mind that your exhaust not is greatly affected by your engine. Heads, rockers and most importantly CAM are all going to make your car very different. No matter what exhaust you have, you aren't going to get the mean lumpy sound with a stock cam.
About all I can think of for now. Pretty sure all that is right, if not someone will straighten me out
www.mustangexhuast.com
www.exhaustsoundclips.com
for different exhaust combos.