Noctua is a bit higher end fan, as it cost near $20, is rated for like 150,000 hrs, which is like 17 years of constant running. Has a some fancy self leveling bearings, frame is designed to smooth and accelerate airflow etc. The stock fan is a generic style case fan worth a couple of bucks, though it admittedly does the job well enough for most purposes.
You get some resistors with the Noctua (in addition to the silicon mounts) that allow you to choose the speed of the fan, which has an affect on noise levels, but also air flow. I run mine at the slightly slower setting, 2000rpm I think it is, and it still moves enough air that my heat gun measurements were the same as the stock fan at higher speed, or when running at the full speed, I was getting a degree or two cooler than stock, so I do think the Noctua's design moves a little more air for a given rpm speed, and/or the fan frame as the design of the blades etc works slightly better.
I've had the bearings go out on the cheaper fans on my Axe II's after a few years. I've used Noctua's in my PC's and switched to them in the II's and they've been 100% reliable (knock on wood). Granted you could buy 2 or 3 cheaper fan for the cost of one of them, but.... if I can spend $20 (or $17.99 I think I paid), spend 5 minutes swapping it out, and presumably never have to worry about the fan for 20 years, and have it quieter, its all and all well worth doing in my book, but everyone has to weight the choice themselves.