You can't access command line arguments for ClickOnce applications directly. To get to them, I used the following, modified a bit from here:
System.Runtime.Hosting.ActivationArguments args = AppDomain.CurrentDomain.SetupInformation.ActivationArguments;
if (args.ActivationData != null)
{
foreach (string commandLineFile in AppDomain.CurrentDomain.SetupInformation.ActivationArguments.ActivationData)
{
MessageBox.Show(string.Format("Command Line File: {0}", commandLineFile));
}
}
This gave me the file name I clicked on. Hoorah.