Assuming you're using Windows 98, I'd do the following (although Greg's response works most of the time, too):
Right before swapping out motherboards, open up Regedit. Go the to key:
HKEY_LOCAL_MACHINE\Enum
Delete the Enum key entirely.
Then, shutdown Windows, power off, replace the motherboard with all your peripherals, powerup...check the bios for anything you need to set there first, then boot into Windows again.
This will ensure that Win9x will make a totally fresh update of all your devices, including new motherboard features, while NOT carrying over any potentially conflicting info from the old motherboard.
Note: Have ALL your drivers ready to reinstall after doing this, 'cuz windows will surely ask for them if they are not part of the operating system.