"Windows could not start because the following file is missing or corrupt: \WINDOWS\SYSTEM32\CONFIG\SYSTEM"

This error arises when the System registry hive is either deleted or corrupt. System registry hive contains configuration information necessary for the system to boot.

Option 1: The first thing to try is to run chkdsk command from the Recovery Console and then reboot the system.

Note: If you don't have Windows installation disk to access Recovery Console, then this ISO image can be used to create a Windows Recovery Console CD. Download the ISO image and burn it to a CD/DVD (ImgBurn can be used to burn ISO images to CD/DVD). Boot the PC using this disk to access Recovery Console.

If chkdsk does not solve the problem, then the System file should be restored from backups. There are two places to look for the backups, one is the System Restore folder and the other is \Windows\Repair folder.

Option 2 (Using backups from System Restore feature): From the Recovery Console, navigate to the folder \System Volume Information\ folder of the root drive, using the command:
cd "C:\System Volume Information"

Here, locate and navigate to the folder whose name begins with _restore using the command:
cd _resto~1

This folder contains many subfolders which have names of the form RPxxx, where xxx is a number indicating the restore point. Locate an RPxxx folder which has the highest number as its suffix (highest xxx) using the command dir command. Then navigate into that folder using the command:
cd RPxxx (don't forget to replace xxx with the corresponding number!)

Now, there will be a folder named snapshot. Navigate to this folder using the command:
cd snapshot

There should be a file named _REGISTRY_MACHINE_SYSTEM, copy this file to the \Windows\System32\Config folder with the name System using the command:
copy _REGISTRY_MACHINE_SYSTEM C:\Windows\System32\Config\System

Reboot the system and check whether Windows loads properly.

Note: Option 2 works only if System Restore feature of Windows XP is enabled. If System Restore was disabled or if option 2 did not work for some reason, then try the next option.

Option 3: While installing Windows, the setup backs up the System registry hive in Repair folder. If the System Restore feature is turned off, then this backup can be used to restore the System hive. From the Recovery Console, navigate to folder \Windows\Repair, using the command:
cd C:\Windows\Repair

Copy the System file to its original location using the command:
copy System C:\Windows\System32\Config\System

Reboot the system and check whether Windows loads properly.

Note: There is a disadvantage in this method! Since this backup is created during the installation of Windows; system configuration and driver installations (made after fresh installation) will be lost after restoring this backup Registry hive file.

More resources can be found here and here.

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Deleted files don’t go to Recycle Bin

Due to some changes in the Windows settings or Registry changes, it can happen that the deleted files or folders do not go to Recycle Bin but they are permanently deleted. These are some of the steps which can be tried to rectify the problem.

Empty Recycle Bin: This may sound simple, but it solves the problem sometimes, so there’s no harm in trying it. Right click on the Recycle Bin icon and click “Empty Recycle Bin” even if it is empty.

Recycle Bin Properties: Right click on the Recycle Bin icon and click "Properties" option. Here, under "Global" tab make sure that option "Use one setting for all drives" is selected and the option "Do not move files to Recycle Bin" is unchecked.

Registry fix: Download this Registry file and save it with the default filename (which has a .REG extension). Double click on it and click "Yes" to agree to merge it to Registry. Restart the PC to make the changes take effect.

Delete the "Recycled" folder: Go to Start > Run and type the command cmd and press Enter key to go to Command Prompt. Here, at the command prompt, type rd /s /q C:\recycled and press Enter key. Repeat this command for all the drives by changing the drive letter in the above command. Reboot the system and check whether the Recycle Bin works correctly or not. For NTFS systems, replace recycled by recycler.

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