According to Wikipedia, the Command key's purpose is to allow the user to enter keyboard shortcut commands to GUI applications. In that way, the Control key is available for its original purpose: entering control characters in terminal applications. It may seem just a detail, especially if you are a Windows user who don't use often the console, but I do, and after a confusing moment, I not only get used to it but now I love it, and I want the Linux desktop environments to behave the same way. Why?
All the terminal emulators that I used on Linux have tabs. As Ctrl+T is a shortcut that can being used by a console application, the shortcut to create new tabs is Ctrl+Shift+T. As this are many more examples (like Ctrl\[+Shift\]+C to copy, Ctrl\[+Shift\]+V to paste...), so I must move a switch on my brain every time that I use a terminal emulator on Linux.
For the contrary, as Mac OS X uses the Command key to send commands to GUI if I want a new tab in whatever application (even terminal emulators) I always use the same shortcut: Cmd+T. It removes all the ambiguity. Think on Windows: some apps uses Ctrl+Y to redo, others Ctrl+Shift+Z, while in Mac OS X always is Cmd+Shift+Z.
It's important for you too!
Although all this could sound a bit geeky, if you are using a browser, the emulation of the Command key in other operating systems could improve your experience. More and more applications will be written for the web, and will have shortcuts, and those shortcuts will collide with your browser shortcuts as already happens. Read the discussion of this Lea Verou post. The irony is that the mess has invaded Mac, because web developers emulate the system behavior instead of the terminal emulator behavior.
If that's is done, there no be more collisions, because Cmd+T will open new tabs in the browser and Ctrl+T will open new tabs in a web app, for example.
Please GNOME, listen to my prayers!
The GNOME project refers to the Command key, Windows key and Meta key as the
System key. I would love the System key behaves like the Command key does in Mac OS X. Is a more consistent and usable behavior, and can solve the web apps shortcut dilemma.