Our client is using table rate shipping method but he needed slightly modification on the default one. They want to set shipping price on the product level (optionally). So, if shipping is defined for the product then use that to calculate shipping of the order.
If the product is set as 'free' then exclude it's price from shipping. If it's left empty or set as 'default' then just use the rate from table. But if the product has custom shipping price, then add that on the shipping.
This is how I modified the magento's official table rate shipping module/extension.
First of all, go to Magento admin / Catalog / Attributes / Manage Attributes and add new attribute with Attribute code 'tn_table_rate' with input type 'Text Field' and label 'Shipping Cost'. Then add it to your Attribute Set.