Here you can configure which clipboard(s) are written or read by PuTTY's various copy and paste actions.
Most platforms, including Windows, have a single system clipboard. On these platforms, PuTTY provides a second clipboard-like facility by permitting you to paste the text you last selected in this window, whether or not it is currently also in the system clipboard. This is not enabled by default.
The X Window System (which underlies most Unix graphical interfaces) provides multiple clipboards (or ‘selections’), and many applications support more than one of them by a different user interface mechanism. When PuTTY itself is running on Unix, it has more configurability relating to these selections.
The two most commonly used selections are called ‘PRIMARY’ and ‘CLIPBOARD’; in applications supporting both, the usual behaviour is that PRIMARY is used by mouse-only actions (selecting text automatically copies it to PRIMARY, and middle-clicking pastes from PRIMARY), whereas CLIPBOARD is used by explicit Copy and Paste menu items or keypresses such as Ctrl-C and Ctrl-V.