Below table illustrates the differences.
|Stsadm Backup/Restore||Stsadm Export/Import|
|Backup\Restore a Site Collection or a Web application.||Exports data of a Subsite, site collection, an entire web application, or a single list.|
|The GUID of all items in a Site Collection is preserved except the GUID of the Site collection itself. When you restore the backup, SharePoint generates a new GUID for the site collection.||It generates a new GUID for every objects such as sites, sub sites, lists and items.|
|Because of the same Guid, you can restore in the same web application or farm but in a different Content database.||Because of the new Guid, you can restore or import the data in the same site collection\site or web application and it does not matter on which content database you run import operation.|
|This operation is designed to take an exact copy of a site collection, no data will be changed, transformed or lost.||This operation is good for merging content of sites, and decide how to handle identical data between source and target.|
|All workflows instances, associations, history and tasks are preserved.||A major drawback of this operation is that it does not preserves workflows instances, associations, history and tasks. Every workflow association must be recreated and there is no way to restore the running instances from original site.|