Comment by ufo

The reason for the confusion is that there are two separate clipboards: one for Ctrl-C/Ctrl-V and one for mouse-select/mouse-middle-click. To use the first clipboard on terminal emulators you need to use Ctrl-Shift-C/Ctrl-Shift-V instead because the Ctrl-* shortcuts have legacy meanings in the terminal. I don't remember ever needing to use Insert for copy pasting (although you can use it if you want).

I don't know what examples you had in mind when you mentioned applications having incompatible keyboards. The only one I know that does that is Vim (which by default uses the internal clipboard when you use its cut, copy and paste commands) but Vim is definitely not your average Linux application...