As long as your new motherboard physically fits your casing, the changeover is not a big deal, as long as you are prepared.
When you change over all the components, the system is going to sense the change and want to load new drivers for them. These items are the ones that typically appear under 'System devices' in Device Manager (Control Panel/System/Device Manager). These usually come on a CD with the new motherboard. Depending on which version of WIndows you are running, this can be messy or not so messy.
Basically, the first time you boot up, Windows will go looking for these drivers, so it's a good idea to copy the contents of that CD (or at least the drivers on it) to an area on your C: drive where you can point it to when it asks. You need to do this before you dismantle your old system. WIndows XP or 2000 may even recognize the devices without asking for any drivers.
The rest of system isn't changing so will be recognized as before.
Another way to do it, or if you have any problems, re-install Windows over the top of itself. This will keep your settings but pick up any new devices, but again have the drivers ready.