Disable Auto Update for VLC Media Player
Answer Chosen by the Author
The first link underneath the Google search has some options for disabling it. None are registry based, but between the three there's an option for almost every deployment.
Edit: I had a little more time, so I did a second Google search for "disable auto update for vlc through registry"and the very first link says that no settings are stored in the registry.
Community Chosen Answer
VLC stores its settings in a binary file called 'vlcrc' which is located in the user profile tree, in '%AppData%\VLC'. Create that on the machine you're building your deployment package with and include it.
If you're re-packaging - and why wouldn't you? - use an advertised shortcut along with the usual self-healing feature set up so that clicking the shortcut installs the file for the logged-in user.