This is what I was thinking of, sorry but I'm not much of an artist. There probably has to be a resistor in there somewhere to limit the current on the base or something. Maybe an optoisolator instead of the transistor?

Okay, how about in parallel? there are 8 120s on two water cooling units(4 on each). Plus there are a few more fans in the case. I know the 3 pin header can't handle much, that is why I wanted to build a unit with a transistor to control the 12v soure(4 pin molex CONTROLLED by the 3 pin fan controll...

First off this stuff is great, thanks. Second, I want to try and build something a little more powerful. I was wondering if I could run the 12v power from one of the three pin fan connectors on the motherboard to a transistor to control 8 120mm fans in series(4 pin molex of course). This way I could...