Are these apps just the Apple-supplied apps (iTunes, iMovie, etc) or all other 3rd party apps that you have added to the system?
2nd question: Why do you want to move any apps out of the original installed locations, when use of an alias will allow you to launch apps from any other folder? The system should not PREVENT you from using an app from most locations on your drive, but, as has been stated here already, some Apple apps (and other apps, too) should normally be left in their original installed locations for updating purposes.