I have the option of using the 4 pin stock cooler or an old 92mm Zalman CNPS7000C-Cu (http://www.newegg.com/Product/Product.aspx?Item=N82E168...) heatsink with 3 pins and a manual speed controller. I'm not sure which one is the better choice for me. Is that fourth pin that the Zalman is missing made up for by the manual control device? I don't really know anything about how to control fan speeds and such so I like the idea of my motherboard doing that for me. However, if the benefits of manual control combined with a better aftermarket cooler are worth it, I can definately learn how to go manual.
(The link in my post is for a re-release of the same model; mine's about 4 or 5 years old.)
The 4 pin header is a PWM(pulse width modulation) header that will accept a 3 pin or a 4 pin fan. If you want the fan speed to be modulated by the motherboard, then you need a 4 pin PWM fan. I personally find it less objectionable to hear a constant fan speed, so a 3 pin fan is ok by me.
The 7000 was on my last motherboard for about 4 years with no warping. I currently own both fans (and don't plan on getting any other ones- I know there are always better alternatives) so I'm just wondering which is better. I don't plan on doing much overclocking, if any. Which is the quietest and the coolest? The Zalman? I'd try both of them myself, but the Zalman has the back bracket which makes swapping out fans a little trickier than most swap-outs.
the easiest way to find out which is better for your setup is going to be try them both. Check the stats of your processor in a hardware monitor program such as O.C.C.T. or hardware monitor or Core Temp. Test them both at load and at idle the best one will or should be apparant.