Remapping keys system wide in linux, not just in X

You will need to use loadkeys for your console. See also keymaps and dumpkeys.

From askubuntu.com

As far as your caps->ctrl goes, this works. You might be able to use this same method to remap your super key as well.

sudo vi /etc/default/keyboard

Now find the line that starts with XKBOPTIONS, and add ctrl:nocaps to make caps an additional ctrl or ctrl:swapcaps to swap them.

For example, mine looks like

XKBOPTIONS="lv3:ralt_alt,compose:menu,ctrl:nocaps"

then run

sudo dpkg-reconfigure keyboard-configuration

The reason this way is better is that it will take effect on the virtual consoles (e.g. ctrl+alt+F1) as well as in the graphical desktop.