MacOS – Change Command Key to Control Key

Keep in mind that the Command key is the same as the Windows key (or Super) in Bootcamp/whatever.

1. Back up. Santa will thank you.
2. Read this guide and this guide if you want to get a basic idea of what I'm doing in step 3.

3. Add these two commands to your startup (System->Administration->Startup Applications):

   xmodmap -e 'keycode 133=Control_L'
   xmodmap -e 'keycode 37=Super_L'
   

   That'll take care of the left side, swapping the Command and Control key functions.

4. Add these two commands to your startup too for the right command and control.

   xmodmap -e 'keycode 134=Control_R'
   xmodmap -e 'keycode 109=Super_R'
   

It'll only work as soon as you log in though.

Answering my own question. :-P

Shortly after posting, I googled across an application called Karabiner that does precisely what I needed it to do (in addition to a lot of other stuff).

Specifically, you can map the left and right Command keys to be Control keys in only Remote Desktop Connection and VMs.