Xorg Keyboard – How to Map ‘Windows’ Key to ‘Ctrl’

xmodmap lets you modify keymaps. Make a file to hold xmodmap commands (~/.xmodmaprc is a common choice). The Win keys are called "Super" in xmodmap (Super_L and Super_R for the left and right ones). By default they're connected to mod4, so you want to remove them from that modifier and add them to control. Add this to the command file:

remove mod4 = Super_L Super_R
add control = Super_L Super_R

Tell xmodmap to load it with:

$ xmodmap ~/.xmodmaprc

It will only last as long as your X session does, so you'll need to rerun it each time, or put it in something like ~/.xinitrc so it will be run automatically