Not all mods equate to better fuel economy. Most of it is just marketing by the aftermarket companies. If it sounds too good to be true, it probably is. If the stock intake is restrictive, the engine will have to work harder to gather air, but this is almost never the case. Same thing with the exhaust. Different spark plugs will not help unless they are misfiring. The problem is most of these mods will help with horsepower at the top of the rpm range, but often times low-end torque is adversely affected. For something your drive everyday you want good low end torque and fuel economy in the low rpm range. Cars are designed to achieve the best fuel economy from the factory nowadays, so most mods are somewhat of a waste. If you just change your air filter and perform regular maintenance on your car, it should get optimal fuel economy. Most of the so called "cold air" intake installs I see are actually "warm air" because they are not baffled properly. You will end up getting worse fuel economy with this setup because the factory intake was cold air already.
For SEAN: Yes, factory intakes are subject to NVH requirements that don't normally apply at all for aftermarket intakes. However, NVH compliance is more a function of tuning the intake with baffles and Helmholtz resonators. The intake diameter is not simply "restricted" to achieve NVH compliance. Remember if you make an intake too big, you will lose velocity and possibly volumetric efficiency. The stock intake diameter is carefully chosen to optimize all these factors. Also, pumping losses and volumetric efficiency has much more to do with the intake runner and head design than the portion of the intake upstream of the throttle body, which would be the difference with a CAI. Yes, the CAI might increase the volumetric efficiency at high rpms, but it might lower it at lower rpms where the car is normally driven for fuel economy. Many forget volumetric efficiency is a moving target that can vary significantly with engine rpm. Getting a consistently high volumetric efficiency across a wide rpm range (with more emphasis on the low end) is what the engineers focus on and is how the stock intakes are designed. I still stand behind my above argument: on modern vehicles you will almost always get the best fuel economy with the stock intake under normal driving circumstances.
As for exhaust, higher flow mufflers can make a difference, but your car might no longer be road legal in all jurisdictions. Companies like MagnaFlow are mostly about making the car sound better. Yes, their mufflers are less restrictive, but again, people don't buy cat-backs for fuel economy because they don't make a big difference at low engine speeds. On sports cars, the stock mufflers are already about as loud as they can be legally, so replacing them might not make any difference in that case unless you're modding a vehicle destined for off road use only. Since the muffler is the main point of restriction in stock systems, increasing the exhaust diameter might not make much of difference either for NA engines (and again, might decrease the exhaust velocity). As for the headers and cats, I shouldn't have to explain scavenging other than to say headers and cats are designed as a unit. If you remove or hollow the cats out with the stock headers, you will probably lose fuel efficiency unless you redesign the headers for use without cats at cruising speed. Again, this is off road stuff and normally doesn't apply, which is why I tell most people to leave it alone if they’re at all concerned with fuel economy.