In Mountain-Lion when a window is closed in any application its almost like the application disapears!
If you want an application's window to move out of the way, click the yellow button. Its window will be "minimized" to the Dock. If you want an application's window to remain open, don't close it.
If an application has no open windows, it has no open windows. That in itself does not necessarily imply anything. The application's previously active processes may remain active, or not. An example is Mail. Closing its Message Viewer window does not quit the app, since Mail has other functions for which their own windows are appropriate.
A different is Dictionary. Closing its window quits the app, since there is nothing for Dictionary to do with no open windows.
Some applications capable of opening multiple windows will quit when no windows remain open. Such features are up to the developer to decide.
Yes, I understand what you're saying, however in many applications when the window is closed the entire app GUI disapears. The app is still running because the name still appears in the top-left of the menu bar, but the GUI is gone and you have to click on the app icon in the Dock to get the GUI to reappear. It's annoying. In pervious OSs when you closed the window the app GUI was still there with all its tools and palets, it was just blank.
In the app's menu bar, select the Window menu to open any previously closed windows. For apps that remain open after all windows are closed, selecting the app in the Dock will open a window as feedback that your action wasn't ignored.
I don't understand the distinction between an app and what you are calling its "GUI". Nearly every Mac app uses windows for their UI, but a open window is not strictly required for an app to function.
What you describe seems completely normal to me; essentially unchanged for every Mac OS since 1985, yet you seem convinced something is different and abnormal in Mountain Lion. Could you help me understand why that may be?
Is it possible the following System Preference (circled) may be applicable to your concern?
I might be getting the wrong end of the stick but is this a case of you using 'A' or 'B' in the below shot?
I liken what you are claiming to how Windows does things in Excle or Word. With an open spreadsheet for example you have two close crosses in the top right corner. The outer one closes the whole program and the inner one just the document.
(to the OP) "B" closes the movie. "A" resizes the whole iTunes app window. Is that what is going on?
Red closes the iTunes window but does not quit iTunes. Yellow minimizes it.
In general, the green button enlarges a window to fill an entire screen, but the green button behaviour has been inconsistent among apps. Different apps implemented different functions for the green button; mostly those for which filling the screen makes little sense. The Calculator app, for instance, has no green button (it's greyed out).
Mountain Lion is making more use of full screen apps - click the circled icon:
Nearly all Apple apps now have a full screen mode as an option. You may prefer to run apps in full screen mode, or in the traditional "windowed" way. If you prefer the traditional look, you may really appreciate Mission Control and Spaces.
I don't know what MS Windows does.
It's similar to what happens with a Windows computer. Using iTunes is the perfect example. Play a music video in it. Then hit the "esc" key to close that playing video window. Instead of returning to the iTunes GUI it closes everything but the actual app. You have to use Mission control, like John is talking about, or click on the iTunes icon in the Dock. Either way, you have to perform an annoying function to return iTunes to a usable state with it's GUI visiable. The app is still running but there is nothing to click on (such as a song or another video) because the GUI is gone. Other apps do this as well. Windows computers does it worse.
Yes, John, I understand Mission control and all the button functions to minimize, expand and full-screen a window. That's not exactly what I'm talking about. It's similar. More what I'm talking about is what happens to the app GUI when a window is closed. As explained in my reply to Gunsie, when using iTunes and playing a music-video or movie. When you close that window, the computer does not return to the iTunes app GUI but a clear screen showing the other apps running below it (or the desktop image). It's apparent that iTunes is still running from the app text in the top-left menu bar, but the app GUI is gone. I have to either click the iTunes icon in the Dock or use Mission control to reselct iTunes by cliking on the icon. Either way, the user has to perfom an unessesary step to return to the actuall usable features of the application. iTunes is the worst of all the apps with this particular annoyance.
I don't think Apple is going to change it.
I gotta admit, it works for me though we're all different. From time to time I click the cross accidentally at work while using Outlook and it closes the whole program. Doesn't sound like a big deal admittedly but when it sometimes take 10 minutes to re-open it's really annoying. Same thing goes for Adobe reader.
It's just something I've gotten used to and now quite like. Using ⌘Q instead of the red X to close apps is now second nature to me.
Beats me FRENZIED.
Closing a window will reveal windows of other windowed apps previously hidden by that window. That is nothing new.
Consider using full screen mode for apps that support it. By providing a full screen mode for all their apps, Apple is clearly encouraging other developers to include this feature in theirs. Since Lion, OS X also provides several additional means of avoiding a proliferation of overlapping and potentially confusing windows, such as the ability to create an unlimited number of additional Desktop Spaces that can be individually selected using a variety of means.
Your Mac appeares to be functioning as designed, so I have nothing else to suggest.