Other responses here are not correct or helpful. It is incorrect to state that it never needs removing.
One such example I experienced recently was when the application had a need for administrative privileges. Any attempt to embed administrative requirements into the manifest will result in the application not even compiling while ClickOnce is still present in the solution.
The following two steps enabled me to turn off ClickOnce (in Visual Studio 2010):
In the project properties,
- Signing tab: Untick “Sign the ClickOnce manifests”
- Security tab: Untick “Enable ClickOnce security settings”