Magento 1 Add Product To Cart w Custom Options [CartController or Observer Methods]

gistfile1.php

$custom_option1 = array('label'=>'Custom1','value'=>$value1);
$custom_option2 = array('label'=>'Custom2','value'=>$value2);
$product->addCustomOption('additional_options', serialize(array($custom_option1,$custom_option2)));
$product->setHasOptions(true);
$cart->addProduct($product, $params);
$cart->save(); 

//USE 'additional_options' if you need the CustomOption to show up on checkout/cart, as $item->getCustomOptions() only looks at 'additional_options' and 'option_ids'

$item->getOptionByCode('option_ids');
$item->getOptionByCode('additional_options');
//in app/code/core/Mage/Catalog/Helper/Product/Configuration.php

//So we can use instead:
$product->addCustomOption('real_custom_option_group',serialize(array($custom_option1,$custom_option2)));

//and to retrieve:
$optiongroup = $item->getOptionByCode('real_custom_option_group');
$options = unserialize($optiongroup->getValue());
foreach($options as $option){
//do things with the $option@array('label'=>'Custom1','value'=>$value1) )
}