It all really depends on the motherboard. My ASUS M5A97 EVO 4-pin CPU fan header doesn't seem to want to control fans via voltages; the other 3-pin fan headers on it will. (Strange, I know.) Inversely, my other build, which is has a Biostar A85W, has a 4-pin CPU fan header that will control fans via voltages, but other other 3-pin fan headers will not. Unless, of course, if there's a better (non-LED) aftermarket fan out there than can spew out airflow higher than the stock's 83 CFM@1800-2000RPM.
As for fan choices, I recommend the Cougar Dual-X fans. The Enermax Vega Duos are good, but they're getting a touch old, and use a manual knob-controller to operate the RPM - it's cool at first, but paired with yet another wire and on/off controller for the lights, it can make for a lot of clutter and inconvenience. Two of them would be a bit much. Also, at full tilt, they can be a bit louder than one would desire.
I have an ETS-T40-TB, the most basic variant, and I like it. It stands up well to any Hyper 212 variant - and I am going to go out on a branch and say yes even the Hyper 212 X. The only issue with the cooler is that it utilizes first-generation Direct-Touch Heatpipe technology - so you have an aluminum strip making contact with the center of the CPU (the hottest part). What this translates out to in real-world experience is that, during heavy-to-extreme overclocking, there are diminishing returns and the cooler starts to fall behind. This sounds worse than what it actually is; the difference generally ends up being a couple degrees.
What CPU do you have?