Allow pop-up's for specific sites using GPO
From either Computer or User section of the approprate GPO, go to....
Administrative Templates > Windows Components > Internet Explorer
"Pop-Up Allow List"
This will apply a registry entry on your client machines at:
[HKEY_CURRENT_USER\Software\Policies\Microsoft\Internet Explorer\New Windows\Windows\Allow]
However, if you are using IE11, it probably wont work as IE11 looks at:
[HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\New Windows\Allow]
In this case, use the "Preferences" section of the GPO to apply directly to the registry......
While testing, I discovered that setting this via preferences and importing a registry key works for IE8 AND IE11 so most likely will work for IE9, and IE10 as well in which case you can forget the official GPO method as it won't work for IE10 and above.