It totally depends what kind of hardware you are connecting to it.
A standard molex connector (4-pin, like the one you plug into your hard drive) carries both a 12v DC line and a 5v DC line. Some devices require both for stability and consistency, such as hard drives, video cards, optical drives, some fans, lights, you name it.
3.3v is for different parts of the motherboard that don't require as much power. It's also used for the LED on the mobo and the LED's on the front bezel.
Intel Q9400 | Gigabyte EP45-UD3P | G.Skill 2x2GB DDR2 1000 | XFX HD5870
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