Honestly, I would say it is a worthwhile investment.
3 pin PWM hasn't changed in forever, and isn't going to any time soon, so it isn't as though it is something you will get rid of in a year or two's time like most of your other components.
You buy a decent fan or two, and no matter what setup you have you are guarenteed good airflow and therefore most likely cooling, and silence. You do not really have to ever worry about case cooling ever again after that initial purchase.
Shop around though, in real world terms, there is little to no difference between the Noctua's, Scythe Glide Stream or Corsair AF's (for your case, not heatsinks)