How does one pass command line argument to a ClickOnce application?

Since you get to the deployment manifest via a Url, you can pass all of that information via the query string (e.g. http://clickonce.example.com/shell.application?p1=this&p2=that)

I was going to type out the steps, then googled and found this blog that basically lists out all the steps. I've done something similar in one instance with no issues. The only slightly difficult thing is that you have to re-mage after setting things up, but if you got it to deploy in the first place, you already know how to set things up.

Good luck!

Perhaps you could pass a parameter on the URL the first time, and have the app take notice of that, and write the parameters to a config file, or environment variables or somesuch.

On subsequent runs, load from the config file

All of the answers here only apply to Online ClickOnce applications. This MSDN Forum post and this blog post discuss some ways to do it for Offline ClickOnce applications.