The first thing to do is ensure Windows is in a state where it can work on the new system. In the case of 2000 and XP, this just means that it has to be able to access the hard drives.
To do this, replace the Bus Master drivers with standard generic drivers, as seen below. The drivers you need to be working on are found in Device Manager under "IDE ATA/ATAPI controllers". Ignore the Primary and Secondary, go for the other one. nForce users will only see one entry per controller.
If you're changing chipset (think in terms of drivers - Drivers for the VIA KT133 work fine with a KT400, but drivers for i815 won't work at all with an AMD760MPX), then you'll want to knock out the AGP drivers too to avoid video problems after the switch. Either uninstall them from the Control Panel, Add/Remove Programs or, in the case of VIA's 4in1, from the driver installation program. If you have neither (ie. SiS, ALi) or just can't be bothered, then observe the illustration below.
The standard PCI to PCI bridge disables everything AGP, but also makes sure that old AGP drivers aren't around to screw your system up.
You should be good to go now, but it's worth it to do some more cleaning up. Remove both USB controllers (don't do this if you have a USB keyboard/mouse, duh) and uninstall your display drivers. Also uninstall any other non-critical drivers from the Add/Remove Programs in the Control Panel, or any other option your driver installer has. They'll need to be reinstalled anyway, since Windows has to reinstall devices if they change INT# lines and they will.