Convert those customers who checked out as a guest to a registered customer. Either convert en mass or convert individually. If a customer is registered already and you wish to associate an old order, you can merge them to an existing customer account. All based around the customer email used to checkout, allowing you to merge multiple orders from the same customer under the same user customer account (as long as they have not changed their email address).
Supports Magento CE 1.3x - 1.7x, Enterprise & Professional