If you're talking about the fan mounted atop the Northbridge of the motherboard, then you'll not have to worry about noise too much. It is pretty quiet.
Of course, if it bothers you, then you can go back to a Pentium2 or something that doesn't require active cooling on the chipset. Due to the great performance that is coming out of nearly all of the modern motherboards of today, cooling has become more important than ever. Your only other option is to downgrade to a point where crappy performance will equate to perfect silence.