Yes you'll have to re-install Windows, but only because you're changing the motherboard, changing just the CPU doesn't require a re-install.
Sometimes you can get away without a re-install but with all the errors that you'll have to deal with it's not worth the hassle of trying. For one thing, Windows Setup has to create a new Hardware ID which is based on the new motherboard, and that ID can only be created by Windows Setup. It's then used to validate Product Activation.
Yes also to re-installing applications and games. There's no way to avoid that with a fresh Windows installation.