Here is one that would cover the rape of Nanking etc.:
Mass executions.
There is a significant portion of the civilian population that is not productive in industry because they are disabled, elderly, children, etc. Nevertheless they consume food and other resources that could be put to industrial or military use. Anytime you capture a territory worth 2 or more IPCs you may opt to hold a mass execution to purge the civilian population of this element and free up those resources. For every mass execution you collect 1 extra IPC for that territory on the turn when it was captured, but you also incur -2 war crimes points.
And here is one for unrest:
Fifth column.
If an opposing power has fewer than 60 war crimes points, you may attempt to foment civilian discontent using your network of spies and dissidents within the civilian population of the opposing power. To do this, you buy “insurrection dice” at $5 each and roll them at the beginning of your turn. For each roll of 6, there is a civilian uprising in one industrial complex of your choosing. During the ensuing riots the industrial complex will suffer damage equivalent to a strategic bombing raid (ie 1d6+2). They also incur -1 war crime point per industrial complex for putting down the rebellion and murdering prominent members of its leadership (ie clergy, union leaders, various malcontents and hotheads).
If the opposing power has fewer than 50 war crimes points, the insurrection starts on a roll of 5 or 6.
If the opposing power has fewer than 40 war crimes points, the insurrection starts on a roll of 4 or greater.
If the opposing power has fewer than 30 war crimes points, the insurrection starts on a roll of 3 or greater.
If the opposing power has fewer than 20 war crimes points, the insurrection starts on a roll of 2 or greater.
If the opposing power has fewer than 10 war crimes points, the insurrection starts on a roll of 1 or greater. This is essentially the collapse of the enemy’s society and its capacity for industrial production. Violent overthrow of the regime is imminent.
and how to pay for your sins
Hearts and Minds:
In a cynical attempt to sway world opinion back toward your favour, you may support humanitarian efforts in territories controlled by you, your allies, or in neutral territories. For each $3 you spend on this you gain +1 war crimes point. Simply declare that you are supporting civilian aid and spend the $3 and you get your morality point. Good for you.