Depends, always used to use a fan controller, but motherboards weren't often the best for either higher speed fans nor, years ago, with much in the way of fan control. These days mobo headers are pretty decent for controlling fan speed, with software in window usually giving FAR more precise fan control than the bios. But depends on the mobo, and software, I still find Asus software to be utterly rubbish, gpu side you've got smart doctor, buggy, horrible, insanely slow to load on windows, incredibly limited, got the UI of a program designed in the mid 80's. Same goes for most of their other software, of which most also require 2-3 services to run all the time for no reason when other 3rd party software doesn't require any of the same things. Gigabyte software is equally garish but much smoother and quicker(last time I used it anyway).
Frankly a fan controller negates many of the problems but lack(except for quite expensive models) real variable control for those who want more airflow in higher loads. Personally the worst thing I find about PC noise is the changing noise, you can get used to most levels of noises, and tones, but when they constantly change up and down its very hard to adjust to the noise. Basically I try and set my fans/computer/cooling so its at one speed, full load, or idle, and I try to get that as quiet as possible. 200Mhz less on the cpu, bit less voltage, and near silence appeals to me far more than some arbitrary number. For gaming almost any chip will overclock well beyond gaming requirements in near silence, with a good enough cooler, of which there are many now.
Basically use whatever is most convienient for you. If you're happy with current noise/airflow, theres no reason to change, if its too loud choose the best method for you to cut down fan speed.
