I keep looking up a command to completely uninstall a ClickOnce application form the Application Cache. If the application is deployed using "Run from the Web" method, it is not available in the "Add/Remove Programs" control panel. To remove it, you have to clear the application cache. An important note: this will remove ALL applications from the cache. That is usually not a problem, since the next time you run them, they will be downloaded.
To clear the cache, run the command "mage.exe -cc" from the Visual Studio command prompt.
Mage is using an API call to accomplish this functionality
CleanOnlineAppCache from Dfshim.dll
You can achieve the same functionality by using a command line tool RunDll32.exe
Or create a batch file with the above command