I've got an app that publishes and updates from an http update location (I publish to the ftp site of the host, and update from the website).
The publish.htm page is very handy as I can install the app on any machine, anywhere without needing media. The problem is, so can anyone else. How can I secure the update location so that only authorized users can install the app without buggering the auto-update feature of clickonce?
If you're still transferring over HTTP, it's as easy as running a traffic sniffing program like Wireshark to see where the application is downloading from. To evade this you'll need to make sure to transfer over HTTPS, on top of whatever obfuscation you do to hide the update location.
Is this an internal application? If so you could just exclude the publish.htm page from your deployment. Then to install you would then just use the application manifest link http://yoursite/YourApplication.application which should kick the install off, this would not affect automatic updates. This may be just enough obfuscation to for your purposes.
Failing that you can dynamically generate the application manifest using a little bit of asp.net which would only produce the manifest for the users you want. The other benefit this has is that you can isolate a small group of users when rolling out a new version.
Just a thought.