You can't backup just the programs so you need to either try to repair Windows as Technotiger suggests or bite the bullet and do it the hard way. There is software available to backup a complete drive with the OS, drivers, programs and data. It's too late to do that when the OS is in trouble but you may want to consider it for the future.
You cannot backup Loaded Programs, these may be lost if Preinstalled. Only way to backup Programs is at the Same Time as You backup the Operating System all done when the Computer is running as it should using Acronis True Image