Copy application data, user data in Windows, and reinstall Windows and applications.  I usually do this to my hard disk about once every six months, or when it gets very unreliable from installing and uninstalling software and hardware on too many times.  Use the Windows Explorer to copy everything that isn't "junk" except the Windows directory/folder and reinstall all applications, etc.  Then make a Windows folder on the destination and selectively copy subdirectories/folder and files with user data from the Windows folder to the destination (to the backup).  These include, but may not be limited to:

    * Internet favorites
    * Cookies
    * Password files (they end in .pwl)
    * Mailboxes and other application data in the Windows directory
    * Netscape
    * ISP Dial-up Network Connection Settings

    If you are doing this procedure for a clean install and it involves wiping the disk clean, it is a good idea to make a backup with MS Backup, which comes with Windows 9x/Me, on a scratch drive or network file server in case you forget something.

Some applications keep data in the their corresponding subdirectories in the Program Files folder; e.g., Quick Books Pro accounting in the Intuit subfolder.  You may therefore want to make a folder Program Files,  appropriate subfolders, and copy the data over.