If you search for “automation” in the F1 helpfile, you should see how it works. There is a little (official) tool named “WendiaAutomationControler.exe” that you can feed with parameters to trigger your client – for integrating CTI (Computer Telephony Integration) applications as well as other tools like Outlook. We just don’t use it because we run POB on a Terminal Server farm.
You should find the tool at ftp://ftp.wendia.com/WFTP/POBG6_Versions/WendiaConsoleAutomationControler/
I just did a quick check (opened an existing Case with it), and it worked pretty well – even with ClickOnce.
For you, the helpfile article “Open a Record from a Link with Automation Controler” should be most interesting. It describes how to register a hyperlink type like “pobg6:” to create internal links allowing you to talk to the POB client in many exciting ways.