Swapping Apple and Ctrl Keys

In the terminal enter:

cat > ~/.xmodmaprc
! Erase existing bindings
clear Control
clear Mod4
! Map key 37 (left ctrl) to Super_L (i.e. 'cmd')
keycode  37 = Super_L
! Map key 133 (left cmd) to Control_L (i.e. 'ctrl')
keycode 133 = Control_L
! And update modifier settings
add control = Control_L
add mod4    = Super_L

Press ctrl+c to stop editing the file and log out and in. Upon login Gnome will ask to accept the .xmodmaprc file. Click on the load button. Done.