We came across an excellent barcode system for the E-Commerce application OSCommerce a few months.
This OSCommerce module basically creates a barcode based on the order_id and prints it onto the invoice or packaging slip. You will of course also need a barcode reader but these can be picked up fairly cheaply nowadays from most computer hardware outlets.
Please note that this OSCommerce module has been developed OSC v2.2MS1 and CVS.
You can read more about this module, as well as download it from here: http://www.oscommerce.com/community/contributions,1218
