The Run command is as follows:
var origFolder = aqFileSystem.GetCurrentFolder()
var strApp = aqString.Quote(strApplication);
var objShell = new ActiveXObject("WScript.Shell");
objShell.Run(strApp + " " + strArgList);
I thought I could just use objShell.Close(strApp) but the application doesn't support this method.
You might not need to go quite that far. If you're using the RunCommand to run your applications, eventually, at somepoint, you'll be using the Sys.Process object to access your application. At that point, simply call Sys.Process('YourApp').Close.