Katsu,
the question seems a bit strange, but I'll give it a try.
In application programs (graphical or 'pseudo' graphical (text windows, menu based) one may or may not use special keys. It all depends on the program being run.
For example, if you start the system admin tool sam in text mode (type the following:
unset DISPLAY
sam &
)
several Ctrl-keys are used for navigation.
On the command line the shell you use interprets your keystrokes. The shell uses an 'editor' mode which may be 'vi' or 'emacs'. Vi doesn't use that much Ctrl-keys, although Ctrl-V (^V in short) is used to input special characters (mostly Ctrl-chars). Emacs does use Ctrl-keys for navigation.
So the answer is: it all depends on the context you're in. Hope this helps
JP.