I was looking for the same thing and found something that works without plugins or other programs. You can do it using the registry as described here.
Alternatively, just create 2 reg files. First the file for switching the Ctrl Key to Alt.
switch_ctrl-to-alt.reg
This adds the necessary key to the registry.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=hex:00,00,00,00,00,00,00,00,03,00,00,00,1D,00,38,00,38,00,1D,00,00,00,00,00
And then the file for switching the Alt back to the Ctrl key.
switch_alt-to-ctrl.reg
This removes the necessary key from the registry.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=-
After double clicking the reg-file you need to restart and you're good.
Do you have problems with this causing the key-up for alt being missed? It's definitely happening for me. – Sophistifunk – 2012-11-27T05:40:32.480