Anything based on a Win9x kernel(95/98/ME) isn't SMP compliant, meaning that it won't do a thing with the 2nd cpu. WinNT/2000 are SMP compliant and can take advantage of a second CPU. Other OS's are available too.
Many of the folks involved in Distributed Computing have dual motherboards to help cut down on space while maximizing the CPU power available. Although the boards are more expensive, consider that a single computer with two processors means that you won't need 2 of many things, that you would need with 2 seperate single CPU machines, for instance cases/video/nic/floppy etc.. you'd only need one of each in a dual box. Currently, I have 6 such boxes at home.