The Super key refers to several different keys throughout keyboard history. Originally the Super key was a modifier key on the Space-cadet keyboard. Recently "Super key" has become an alternative name for the Windows key when using Linux or BSD operating systems or software that originated on these systems.
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Knight Keyboard to the Space-cadet Keyboard
Tom Knight created both the Knight keyboard and the Space-cadet keyboard. The improvement from the Knight keyboard to the Space-cadet keyboard was the presence of two more modifiers for the bucky bits, Hyper and Super; the Super key modified the third bucky bit (representing a 4). From the usage of the Space-cadet keyboard on Lisp machines the Super key was inherited by Emacs as one of several supported modifier keys, most modern systems have to emulate the Super key using another.
Linux and BSD
Due to being designed at the time of the Space Cadet Keyboard, X11 defined the shift states "Meta", "Super", and "Hyper" (along with "Shift" and "Control" and "Alt" which were commonly available on keyboards). Initially on PC hardware it was just impossible to produce these shift states as there was no key to push for them. The only software that commonly used these modifiers was Emacs.
With the appearance of keyboards with the Windows key there was now a key available on standard keyboards that could be used for one of these. Initially (in 1996 or so) it was most common to make this key be the "Meta" shift key. However, due to the high number of Emacs commands using "Meta", there were already long-established replacements (the Alt key acted as Meta, or typing Escape,X acted like Meta-X), so adding an actual Meta key did not provide much added functionality. This made Super the first key that there was interest in emulating, and therefore it became the standard assignment after a few years.
To avoid using a Microsoft trademark, much Linux documentation refers to the key as "Super", usually confusing users who still consider it a "Windows key". KDE Plasma documentation it is called the Meta key even though the X11 "Super" shift bit is used.
Most Linux desktop environments use the key similar to how Windows uses it, for window management and application launching, rather than commands used by applications themselves. A popular non-Windows style use is to modify mouse drags so that they move or resize windows from inside them, rather than requiring clicking on the window borders.
In GNOME 3 letting go of the Super key defaults to showing the activities window.
In Openbox the Super key is an available modifier key but is not used in any default shortcuts.
Under Unity the key is used to control launcher and manage windows.
macOS
X11 emulation on macOS puts the Super shift state on the Command key. Since macOS uses the Windows key as the Command Key if you plug a non-Macintosh keyboard in, this means that the layout on such keyboards is the same for macOS and Linux.