From time to time I have found it necessary to change the PNAgent configuration globally for end users, or for particular users.  This is pretty easy to do using a combination of login scripts and registry merges. The difficult thing in recent years has been the changing of the location of the configuration options based on the version of the client or XenApp plugin you were dealing with.

I stumbled across this the other day and hope it will help somebody else as much as it has helped me.

registry locations that control PN Agent