Since my comments are clearly being ignored, I am going to provide some backing to my reasoning using Apple's official OS X Human Interface Guidlines (HIGs).
Every single mac app, according to the HIGs, has an "App Menu", which is the menubar item that says "Minecraft" in this case. This menu is expected to contain "About AppName", "Preferences...", "Services", "Hide AppName", "Hide Others", "Show All", and "Quit AppName" (1). While Minecraft has all of these, the Quit menu does not function.
The Quit function also appears in the HIGs' list of Standard Keyboard shortcuts. If you scroll down to the letter Q, you will see that every Mac app is expected to use Command-Q to quit (2).
It has also been made clear that the reason that the Quit function does not work is that people believe that the OS simply stops the process. This is not the case whatsoever. As seen in the screen recording on source 3, the Quit function does not stop the process. The example I used to create the screen recording is saving a document. If the OS stopped the process when the Quit function was executed, I would not be prompted to save the file.
These are system-wide functions that all Mac developers are expected to follow and, therefore, this should be added to the Minecraft Mac client.
Sources:
1. http://developer.apple.com/library/mac/#documentation/UserExperience/Conceptual/AppleHIGuidelines/Menus/Menus.html#//apple_ref/doc/uid/TP30000356-CIHDGFJB
2. http://developer.apple.com/library/mac/#documentation/UserExperience/Conceptual/AppleHIGuidelines/KeyboardShortcuts/KeyboardShortcuts.html
3. http://youtu.be/45GDEclqQNg
So, we're just going to ignore my comment?
You can set it up to run the clean shutdown on Quit. The OS doesn't just kill the processes when you use Quit. If it did, you wouldn't get a window to make sure you've saved a document in Word (or any document creation tool). This is an OS Default and needs to be implemented. Every single Mac App supports Command-Q.
Sorry about that. I tried to find it but I searched "command" and not "cmd"
Can someone please read my comment on the other issue? This really needs to be fixed, and I have perfectly good reasoning behind it, but no one seems to be watching the issue. https://mojang.atlassian.net/browse/MC-594