If this is from Windows install media, and often from OEM recovery mechanisms also (but not always), during the install you can choose the level of destructiveness you're looking for.
There will be a screen where you can choose not to wipe out the existing installation, but instead overlay it with a clean install of Windows while maintaining the rest of the drive contents. (As opposed to formatting and installing to an empty volume.)
That being said, two warnings:
1. BACK UP YOUR DATA FIRST ANYWAY. MAKE TWO COPIES AND TEST THEM.
2. You'll have to reinstall applications in most cases because the registry will be overwritten anew, even though the contents of "C:\Program Files" will still technically be present. So prepare for that. Same goes for any customization of Windows settings.--
Scott Brown Consulting