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Depends on what vehicle we're talking about and the specifics of the mods. A number of years back Hot Rod did a flow bench test of various OEM and aftermarket "performance" cats to determine which had the best flow for a given pressure drop and IIRC a number of OEMs came out on top (Dodge Viper was one?).
Mufflers are a different can of worms because there's so many different designs its hard to say what's better in which situation. It's true that backpressure is bad and restricting flow at all is inefficient, but any exhaust system at all will have some backpressure associated with it. The acoustical tuning of an exhaust system can have a significant impact on your torque curve and can even flatten the peaks and broaden the curve without changing the cam profile.
A long-tube header 4-1 or a tri-y header 4-2-1 are different ways of trying to do this that will allow some acoustical tuning to shift torque lower in the RPM range. "Shorty" or block-hugger headers offer nothing but a prettier and possibly lower restriction option to cast iron manifolds on 30+ year old engines.
I would be wary about saying aftermarket is lighter. Many aftermarket systems have dual outlets where the stock system would have a single outlet. Often it's added weight for no benefit.
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