My personal experience is that 3-pin runs off voltage not PWM.
I recently set up the Akasa splitter to run 2 apache case fans in my Antec p180 along with the Zalman 9500 cooler. The Zalman is 3-pin and it basically seems to run at max speed always, even when the case fans are changing speed on PWM. I've surmised this is because the 4th pin is the PWM pin and the power from the molex on the splitter is constantly at max.
The only way I can get it to turn down is by putting the fan controller between the splitter and the cooler. I then turned the controller down to minimum and left the case fans on PWM, because the cpu fan is loud and the case fans aren't, and the apaches spinning up to 100% - combined with the cpu fan running low- seem to provide sufficient cooling at full load.
I didn't even realise 3 pin fan connectors existed when I bought the things, I believed they were all 4; but I seem to have found an acceptable solution.