There are two ways by which you can achieve this.

1. Using observer concept.

class Vendor_Namespace_Model_Observer
{
	public function customfunction($observer){
		try
		{
			$item = $observer->getEvent()->getQuoteItem();
			$item->setData(‘customvariable’, ‘somevaue’);
			$item->save();
			return $this;
		}
		catch (Exception $e)
		{
			echo $e->getMessage();
		}
	}
}

2. Another way is to create or custom add to cart function and place following code after add to cart.

/* The following code will set custom value to sales flat quote item start */

$quote = Mage::getSingleton(‘checkout/session’)->getQuote();
$_item = $quote->getItemByProduct($_product);
$_item->getProduct()->setIsSuperMode(true);
$_item->setCustomvariable(“somevaue”)->save();

/* The following code will set custom value to sales flat quote item end */