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Command line reference: Web, Database and OS scripting.

Где Windows хранит расположение иконок десктопа?

Оригинал статьи находится здесь.

The settings for desktop icon placement in Windows XP (or Vista) are located in the the

HKCU\Software\Microsoft\Windows\Shell\Bags\1\Desktop 

registry key.
This registry key contains a number of values, the most relevant if which are the ItemPos<screenresolution> values, the Sort value and the FFlags value.
The sort value controls the sort order of the icons (by name, by type, by size etc.), the FFlags value controls the arrangement of the icons (align to grid, auto align etc.)
Finally there may be any number of ItemPos values (appended with different screen resolutions eg. ItemPos800x600), which control the user defined positions of the icons for different screen resolutions.
For more details about the content of HKCU\Software\Microsoft\Windows\Shell values:
ShellBagsView v1.05

Regarding the Icon view used for any folder of one's choosing, I believe the position of icons would be stored in:

HKEY_CURRENT_USER\Software\Classes\Local Settings\Software\Microsoft\Windows\Shell\Bags\[x]\Shell\{yyyyyyy-yy...}\ItemPos

with 'x' representing one of your many folder specific settings.

Добавлю, также, что в Microsoft Windows NT Resource Kit tools есть расширение shell для сохранения и восстановления иконок десктопа, см. здесь.