After reading MM&FF's CAI article about a year ago (they tested a bunch of them on an S197 GT at the dragstrip - the real world dyno) I became very skeptical of CAI's doing anything other than looking cool. Good read that kept me from throwing away a few hundred bucks on a CAI. The only CAI that added any performance above and beyond the tune by itself was the WMS front-mounted ram air unit. MM&FF showed a real improvement in the 1/4 mile with this one, while all the others showed no improvement. If you have to get a CAI, this should be high on your list.
When I bought my 07 GT, I started looking at the eye-candy that is CAI. The company I bought my DiabloSport Predator tuner from claimed it was good for up to a 27hp increase. They also sold a package that included the C&L CAI and Predator, and claimed it was good for up to a 31hp increase. That tells me that the CAI was worth 4hp. Yikes, that's a lot of money for 4hp. So I passed on the CAI, and bought just the tuner.
Now, for those who choose to get the CAI anyway, you have to tune for it or you'll run lean. I did this on my 03 Mach 1. Bought the C&L TrueFlow inlet tube and big MAF. They were advertising that piece as "no tune required." WRONG! My car slowed at the dragstrip from 13.0's with the stock stuff down to 13.7's with the C&L. The car was so lean it was pinging for most of the track!
Same is true for axle-back systems. They sound cool and some are lighter than the stock mufflers, so that's a plus. However, MM&FF tested them on the S197 GT last year (quite a few of the popular axle-backs), and found most only gave a couple hp, while many lost hp. Most lost torque (need that back pressure to keep torque in check). So, chalk up the axle-backs as "ear candy" and CAI's as "eye candy."
Now, if you have a heavily modified car, then CAI's and exhaust mods will become necessary and will hold real benefits. But, on a mostly stock car, better to leave the factory plumbing intact.