This (raw) screencast shows how to calculate shipping based on weight of items in the order.
We add a weight field to the product, and then create a "calculation rule" for shipping that walks the line items on the order, checks to see which items have a weight, and for each of those adds more to the price of the shipping line item.
I've posted the result of this as a little feature module, drupal.org/sandbox/rfay/1374058
It was inspired by the questions at drupalcommerce.org/node/1721
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