Ninite can disable the built-in automatic update features of some applications.
It works via the /disableautoupdate switch and currently supports these apps:
* iTunes update and Apple Software Update will be disabled. The QuickTime update check cannot be turned off.
Other applications are unaffected by this switch.
Here's an example command:
NinitePro.exe /select Firefox Flash /disableautoupdate
It installs Firefox and Flash with their built-in auto-update mechanisms disabled. You can then fully manage the software updates with Ninite.
These features are only available in Ninite Pro Classic.
We're working on documentation for the new Pro web interface. For now the available help for that is inline in the interface.