Some shipping scenarios require that shipping costs be added after the order has been placed by the customer.

If certain orders through your site have to have shipping added later, set up a shipping method with a descriptive name (such as "Will be Determined when Shipped") and set up your shipping/products so that those special orders only qualify for that shipping method.  Then customers can choose that method during checkout, and will not be charged.  Once the shipping costs have been calculated, they can be added to that order with an adhoc charge.

Note:  This will not work if you are using realtime shipping