It's up to the terminal to decide how to interpret them, not emacs. You'd have to look at the docs for whichever terminal emulator you're using. xmodmap is by far the easiest solution, but some sophisticated emulators should let you rebind there.

setxkbmap Example:

# left ctrl is hyper, caps is control, menu key (next to right ctrl on  my keybord) is another super
# check the man page of `setxkbmap` and grep
# /usr/share/X11/xkb for options
setxkbmap -layout us -option ctrl:swapcaps_hyper,nodeadkeys,nbsp:level3,altwin:menu_win

ah I see I didn't know you want a solution for emacs only