Originally posted by Adeptus
In general, you should not expect to replace the motherboard and have your existing Windows installation just happily adjust to that, unless you are replacing a failed motherboard with the same exact hardware. That hasn't worked worth a damn on any NT-based Windows version ever (which is all Windows for the last 9 years or so).
Whenever possible, I would suggest to back up your data by whatever means available and do a clean installation. If not, you will usually at least have to re-run setup from your Windows DVD and pretend you are doing an "upgrade". Be aware that this solution, which used to work fairly well for prior Windows versions, is reported to have a worse success rate with Windows 7 -- it doesn't hurt to try, but you may end up going through it and still have an unbootable system.
This is one of the things Windows does incredibly poorly and Linux does incredibly well. Windows stores its driver configuration and shits itself when it encounters hardware required for the boot process that doesn't work with the expected driver set. Linux detects anything for which the drivers are built into the kernel or supplied as available modules, on the fly on every boot, so as long as you plan ahead, you can pull off a 100% hardware change without any consequence. With Windows, that only works when you get lucky through backwards compatibility (e.g. your new motherboard uses a chipset that directly descends from the one being replaced).
Since this was the first time I've replaced my motherboard I've learned a lot. I'm glad you mentioned that Windows doesn't adjust very easily to these kind of changes because when I began this I started to encounter a "Your version of Windows 7 is not genuine" and I was being accused of pirating. I'm pretty sure that's been resolved though.
Thanks for the advice, hopefully I wont have to do this again for awhile.