I used to just change the driver for the hard disk controller to the generic PCI one from microsoft before swapping the motherboard. I think the only time it doesn't work is when you're using a weird controller...hell, I've even swapped from an onboard to PCI card based one.
This doesn't do you a shitload of good when the motherboard spontaneously dies on you though. I bet if I added another hardware profile...
Anyway, I read the other day that windows 7 is suppose to be much more friendly about this. Which is nice, since this used to work on 9x systems with no advanced planning but never worked on 2K and up.