If it is not possible to boot in safe mode and last known good configuration is damaged then you can restore the system files from a full registry backup created before Registry First Aid registry scan. If you remember, you were prompted to create a backup of the system state.
In this case you need a second operating system of the same version installed on that machine. You can either install a new OS into another folder (not C:\WinNT originally) or another partition or connect hard drive to a machine with the same Windows version installed.
Windows 2000/2003
Boot into your parallel installed system and launch the Backup utility from the Programs -> Accessories -> System Tools menu. Click on the Restore Wizard button and select the backup file created before. You may be asked for original container of backed up files - select your problem Windows folder.
Windows 2000/2003/XP
If you have no backup files created before the problem then you can restore your system to the state that was just after installing Windows. Then you will probably need to re-install some programs again.
The instructions below will show you how you can replace registry files with backup copies. You need either parallel installed system or install Recovery Console.
Read this topic on how to install Recovery Console and how to use it.
Boot into your parallel installed system, open in explorer your problem Windows folder and find the folder named "Repair" (C:\WINNT\Repair). This folder contains registry backup files created at the time of system installation. It may also contain the "RegBack" subfolder with backup files created by Backup utility.
Please select View -> Details from the explorer window to see file creation dates. Find the most recent file with the name "system" from these two folders ("C:\WINNT\repair" and "C:\WINNT\repair\RegBack") and copy it to the "system32\config" directory ("C:\WINNT\system32\config"). If this folder already contains "system" file then rename it to "system.bak" before.
All of the mentioned above folders (C:\WINNT\repair, C:\WINNT\repair\RegBack, C:\WINNT\system32\config) may contain other registry files: "default", "sam", "security", "software", "system". Try to restore first the "system" file and test loading the system. Only if this didn't help then try to restore other registry files one-by-one with testing between restoring.
"system" file is the "HKEY_LOCAL_MACHINE\System" registry hive, "default" is the "HKEY_LOCAL_MACHINE\.Default" hive, "sam" is the "HKEY_LOCAL_MACHINE\SAM" hive and "security" is the "HKEY_LOCAL_MACHINE\SECURITY" hive. Both last mentioned files contain system security records. Don't modify these files if you don't know what you're doing exactly.
File "software" is the "HKEY_LOCAL_MACHINE\Software" hive. It contains registry keys for installed software. If you replace this file then you will have to re-install the most of your programs.
If any of this doesn't help you then your problem was coming not from registry but from damaged system files. You may need to reinstall your system to restore system files.