If Windows NT or Windows 2000 fails to boot, reporting that the SYSTEM registry hive is corrupt, the proper practice is to restore the System State from last nights backup, or use the ERD (NT 4.0). In a pinch, tip 0505.
As a last resort, you could rename SYSTEM.ALT to SYSTEM, by booting to an alternate install and navigating to \System32\config of the corrupt install.
When you shutdown, the SYSTEM hive is updated with changes. After this is done, SYSTEM.ALT is also updated, so in case of a power failure, hardware or software problem, a good SYSTEM hive would exist.
If the corruption occured during the last shutdown, your SYSTEM.ALT may be ok.
NOTE: In Windows 2000, if your ran a Fast Repair from the recovery console, it would replace the corrupt SYSTEM hive with a copy from %SystemRoot%\Repair\Backup. This is likely to be just as bad, as your SYSTEM hive is now 'mismatched'. In this case, you need to restore the System State.