I found it is entirely based how restrictive your loop is.
As an example:
I am running 2x D5's with the EK tops on the CPU loop.
CPU Block is a XSPC RayStorm and there are 2x 120.1 rads. Initially these were the Black Ice Stealth GTS120 but now are XSPC RX120.1's.
Running both pumps on "3" setting with IBT maxing out 8 threads on the CPU (now a 2700k running at 5Ghz). Changing the pumps from "3" to "5" instantly lowers the load CPU temp by 2C. Cofirmed with Open Hardware Monitor, CoreTemp and RealTemp.
Switch it back to "3, temps instantly go up 2C. Tried this several times with the same result.
This loop is obviously designed for high flow. I am hoping to get my hands on the new Swiftech GTZ block soon. These are MUCH more restrictive so the extra flow is going to be crucial to maintaining a decent temperature.
The myth that a slower flow rate is better as the water has longer to cool down has been around as long as watercooling and pc's themselves. Its all about finding the balance based on the radiators, blocks, pumps and fans you have.
EDIT To summarise, I run both pumps on CPU and GPU loops (4x D5's) all on "5" on foam paddings and they are inaudible.