when changing a motherboard, it can be an issue with your OS as well as drivers. I'll assume you are using XP which is dependent on your hardware. If it is home edition or an OEM it will need to generate a new registration key for your online registration. Odds are it will not work after the motherboard is replaced and as suggested a new copy of windows will need to be installed.
If you want to take your chances, i would suggest partitioning the drive and saving data to the new partition, but do not remove windows just yet. uninstall all 'port' drivers, under device manager and add/remove programs. This includes usb, seriall, etc (there could be others). It may be advisable to remove all printer and video card drivers which are dependent on the drivers you are removing.... thus making a re-install just as reasonable.