Is there any way we can retrieve the list of Published Desktops and Applications from Vmware View Horizon Server
Can you clarify what you are asking? Are you asking can you see a list of published desktops and apps from a Linux Desktop that has the 4.6 client installed? If that is the question then yes you can.
If you are asking to see all published desktops and apps from the client even if they are not assigned to the user then no.