Since Win95's Start Menu (I'm sure there are perhaps earlier examples in other desktop environments, but Windows is what I'm familiar with), users have been encouraged to keep documents on the desktop, and keep application shortcuts filed away in the Start menu or on the Quick Launch bar or other similar launcher. OSX and various Linux desktops are organized in the same way: you can put application shortcuts on the desktop, but the desktop is better for documents.
Why did this happen? A)Even for non-tech-savvy people, the idea of a "file" makes perfect sense if you think about a document, B)Someone realized that opening a document in an application made for that kind of document should be a first class action, and shouldn't necessarily require you to first open the application and then use the application to open the document, and C)When you start putting documents on a desktop, putting "applications" alongside them using the same visual representation (a clickable icon) can be confusing. The result was a more literal "desktop," complete with your click-to-open documents laying around. Tools (applications) were put away in the desk drawers, so to speak.
The widespread usage of iOS has put apps front and center again, both figuratively and literally - users have again become accustomed to seeing grids of icons for their applications instead of their documents. This is reflected in the Ubuntu and OSX screenshots.
users have been encouraged to keep documents on the desktop
Almost every piece of windows software I can remember installing has asked me if I wanted to create a desktop icon for the application. I have a whopping...2 documents there.
This hasn't required any special effort on my part, many applications default to saving in the user or (later) 'My documents' folders. I typically open documents from the file manager or via a 'Recent' menu, but prefer to launch the app if I starting a new document, and can't say I've noticed an irresistible trend for doing things the other way - if you ask me, it depends on the person rather than being driven by the OS.
The main way of launching applications in Program manager was a program containing a grid of applications. Replacing the Applications menu with a dedicated grid of applications for Ubuntu, Applications folder with dedicated grid of applications for OS X. Which is basically what Program Manager was.
(Yes, I know plenty of people probably do this ad hoc with their desktop anyway, but you were _supposed_ to use the proper methods)
