Each application is independently responsible for binding keystrokes to specific operations. While there are conventions (e.g. Ctrl+C is sometimes copy), sometimes different choices are made (e.g. Ctrl+C is sometimes EOT (end of text)).
Applications that are made for a given desktop environment (e.g. gedit Text Editor for GNOME) are very likely to inherit keybindings for that environment, but applications that use different frameworks (e.g. Netbeans for GNOME) are less likely to do so, although some conventions may be followed (i.e. Ctrl+C is copy for both gedit and Netbeans).
Some applications or frameworks may support additional keysyms (like
XF86Copy for copy in gedit Text Editor (usually a dedicated Copy on the keyboard), whereas others will not (Netbeans ignores
XF86Copy). If you have customised keymappings, or complex input devices with special signals (like Copy), you may need to configure support separately in separate applications.
If a specific application does not support some key, and does not offer a way to configure a keybinding for that key, please file a bug requesting support for the appropriate keybinding.
If a specific application does not support some key, and does offer a way to configure a keybinding for that key, consider opening a bug to modify the default configuration to support that key, if you believe this would be a common keybinding, to be expected by default.
If you have specialised input needs (you do not believe that others will want this keybinding), and the application does not offer a means to configure the keybindings, you might open a bug requesting support for configurable keybindings.