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As of Geogebra 3.2.4X there is a new installer that is being used. Just use GeoGebra-Windows-Installer-3-2-46-0.exe /S for a silent install.
Note: Capital "S"
GeoGebra-Windows-Installer-4-0-32-0.exe /S works fine for silent install but places the shortcuts in the root of All Programs menu. Uninstall with commandline "C:\Program Files\GeoGebra\uninstaller.exe" /S doesn't seem to work.
Therefore it is better to create an msi through the snapshot method. This can be done very straightforward by just snapshotting the programfolder and programmenu. No registry entries, ini files or other files are required.
To avoid message about new version 4.0.32 add registry entry:
An official MSI for deployment via AD-GP or SCCM is available from here: https://code.google.com/p/geogebra/downloads/list?can=3
Note that it is not listed on geogebra.org
/S switch stuffs up the shortcut placement: no shortcut is placed on the desktop, and the Start Menu shortcuts are all placed in the root Programs folder instead of its own Geogebra folder.