Windows 2003 could not start because the following file is missing or corrupt:
 \WINNT\SYSTEM32\CONFIG\SYSTEM
I was able to solve it using following method. (I thought it might be useful to share this knowledge for others)
  1. Start the computer by using the Windows 2003 CD. At the “Welcome to Setup” screen, press R to repair, and then press C to start the Recovery Console.
  2. Type the number for the appropriate Windows installation, and then type the Administrator account password.
  3. To copy the SYSTEM file from the WINDOWS\Repair folder to the WINDOWS\System32\Config folder, type the following command, and then press ENTER:
    copy c:\winnt\repair\system c:\winnt\system32\config\SYSTEM
    If you receive a prompt to overwrite the file, press Y, and then press ENTER. (You can also copy all the files one by one, as console doesn’t allow you to use * wild card )
  4. Restart the computer.
And you will see your windows booting normally.

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