I don't know if this is the best way but I am thinking that in the SOQL query editor, you could have a new button for Insert Fields. When clicked, it would pop-up a new window similar to the Pull Data From SFDC or Project Metadata pop-ups.
At the top would be a drop-down control containing all the standard and custom objects in the org. In the middle would be a set of checkboxes, one for each standard and custom field in the selected object type. At the bottom would be a text area that contains a comma-separated list of each checked field. Maybe a "Copy Fields" button at the bottom that puts that text area to the copy/paste buffer. Probably include " from object_type__c" and the end, maybe include the "select " at the start.
This would make it a lot easier to build queries. Today, I have to flip back and forth to the object definition file to copy out the API names into the SOQL.