Many good suggestions here. I had to “repair” Windows with the disk.
Image the OS partiction, as a minimum.
I image mine periodically after some major program installations and clean ups.
Those images (both laptop and desktop) have saved me many times. It is a lot easier to reimage the OS partition than to spend several days reinstalling.
I also keep my data on a separate partition and USB backup drives. If my boot up hard drive fails, I have the image and data backups.
Windows has am imaging program. I have used it a few times, but IIRC, it will not recognize a USB drive.
I currently use Macrium Reflect Free Home edition on my Win7 laptop and desktop.
http://www.macrium.com/reflectfree.aspx
Did you install/update anything just before this happened?