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 Chrome Flash /disableautoupdate
It installs Chrome and Flash with their built-in auto-update mechanisms disabled. You can then fully manage the software updates with Ninite.