Not out of the box, but you can attach a custom form to a Company with drop-downs for 'Parent Company'. As you can set permissions based on Company but not a custom field You would have to:
Maintain the drop-down list for parent companies (at least until the 'Company' object is added to the type ahead field)
Create specific reports to filter on Company OR Parent Company, and run these with permission of someone who can see everything
Barry Buchanan - WMA Work Management Australia