This method has worked for me:
1. Remove all cards except video card.
2. Remove all drivers that you can find, including chipset drivers.
3. Go into BIOS and disable everything you don't need to get into Windows. Boot into safe mode and clean up drivers with Driver Cleaner Pro.
4. When you start up after installing the new motherboard, go into BIOS and, again, disable everything you don't need to boot to safe mode. Sometimes it will fail on first attempt to enter safe mode, so keep trying. Once you get into safe mode, restart and boot Windows normally. Install chipset drivers, reboot, then start enabling things you need in BIOS. You might get better results if you enable and install driver for one device at a time.
5. If it fails to initially boot into safe mode at all, insert the Windows CD and proceed as if you're going to reinstall. When it finds the existing Windows install, it will offer you the option of repairing the existing install, and do so. All programs and files will remain intact, but all Windows updates and drivers will be removed. Sometimes even this doesn't work, in which case you'll want to format and install fresh.