This would a mod allow to choose what happens with the recipe ingredients after crafting. I need this to damage items in crafting recipes. I know I can set the container item but what if in one recipe it should get damaged and in another it shouldn't.

Already possible by implementing ICraftingHandler and registering it:

@Override
public void onCrafting(EntityPlayer player, ItemStack item,
		IInventory craftMatrix) {
	// TODO Auto-generated method stub
	for(int i=0; i<craftMatrix.getSizeInventory(); i++) {
		ItemStack itemstack = craftMatrix.getStackInSlot(i);
		if (itemstack != null && itemstack.getItem() == yourItem) {
			itemstack.damageItem(1, player);
			itemstack.stackSize++;
		}
	}
}

Didn't get the idea to increase the stack size... thanks.