Making the Windows install platform-agnostic
Once that reboot is out of the way (oh, you'll be doing a fair amount of rebooting) launch Device Manager (devmgmt.msc), and replace your onboard storage controller with "Standard Dual Channel PCI IDE Controller," or similar, as shown in Figure 1 below. If it is not listed with the Show compatible hardware checkbox filled, your system may not survive this process unless the new motherboard is from the same chipset vendor.
Figure 1
If you're still on an AGP system, you'll want to knock out your AGP drivers in the same manner, but this time the driver to install is "PCI standard PCI-to-PCI bridge".
Now if you're on an Intel board, you'll need to enable Show Hidden Devices from the menu, and have a look in the new tree which appeared: "Non-Plug and Play Devices". There are two drivers known to cause problems, 'IntelIDE' and 'IntelPPM', so you will need to uninstall them.
At this stage you may also want to remove your video drivers, since they'll likely need reinstalling anyway.
Reboot your system for the driver changes to take effect. Now your system is platform agnostic, you could take the hard disk out and put it pretty much anywhere. The one caveat is that you can't change where the HD logically is, so if you take a HD from the Primary channel (Yes, SATA can still appear to have Secondary and Primary, so check which one your HD is on) to the Secondary, it still won't work. Most will have it as SATA0 or Primary Master/ Transfer this placement exactly to the new motherboard. If you get a boot problem after performing your motherboard swap, this is the very first place to look.
Now power down and do what needs doing, namely the hardware installation.

