For Windows 7 it should work fine but I'd do a few steps before transplanting the motherboard.
1. Take a system image. The system image tool built into the "Backup and Restore" utility will work fine for this.
2. Uninstall drivers for any hardware that won't be on the new motherboard. This includes the video driver if you're moving to a motherboard or processor with a different video chip (e.g. from Sandy Bridge to Ivy Bridge)
3. Update the drivers for any hardware that is the same.
After the motherboard transplant you'll probably need to re-activate Windows which may be a bit problematic if you're running an OEM version.
I've done this on my main system to upgrade to Ivy Bridge and haven't run into any issues (yet).