I'd usually set some command line arguments to the application which I want to start minimized on Windows startup, but a ClickOnce application does not accept parameters when you launch it through an application-reference shortcut.
Is there aother way to make an application start minimized? Starting the application by URL (with URL parameters) is not an option for me, because there's no guarantee that user will have an Internet connection on Windows startup.
It's a WPF application. To make the application start with Windows, I put a registry key to the application-reference as described in ClickOnce and startup on Windows logon (Vista).
As long as you are using at least .NET 3.5 SP1 you can pass parameters to the app-ref shortcut, see How to pass arguments to an offline ClickOnce application or if that's TL;DR see ClickOnce appref.ms argument