Harvey's suggestion to start by making a mirror of your current HDD is excellent, but I think you could benefit from a little expansion on that thought.
If you are running a Windows 9x operating system, it will work perfectly . . . all you have to do is give it the CD that comes with your new motherboard, and all will be well with the world in 3 or 4 reboots.
HOWEVER, if you have WinXP, there are a whole different set of problems you need to consider, which is why the mirror drive would be absolutely necessary. Remember, because of Activation you cannot move your operating system to a new computer, which is what you are doing when you replace the motherboard.
I am assuming that in doing so you will also be upgrading the CPU to something a little faster, and of course, a couple of newer and faster sticks of memory, plus the video, chipset, sound and NIC will be different . . . in other words, a brand new system as far as WinXP is concerned.
Under the older operating systems, if I would be building, say for example, 10 new systems for a client. There would be nothing, for all practical purposes (except for ethics), to stop me from getting one computer up and fully loaded with OS and sortware etc. and then mirroring it to the other 9 HDDs. Many less than ethical individuals (and smaller computer shops) did this, and this is exactly what caused Microsoft to come up with this this annoyance.