They mean the same thing, and can be controlled by the mobo.
Originally Posted by Faster_is_better
I'm fairly certain wire color does not matter, it varies by manufacturer.
Also to answer your original question. 3 pin molex is powered direct from the power supply and runs full speed always(unless connected to fan controller or has switch attached). 3 pin is powered from small 3 pin connectors off the motherboard and can be controlled via BIOS or software utilities generally.
Edit: added more info