If you just want to organize them conveniently, you can simply group them into a new group (or several, if needed). To select all objects within a group, first, switch the Outliner's Type display mode to Groups, then click on the icon(s):
If you want to remove them out of those empties, you can press Shift Ctrl A to make all selected duplicates real, instead of instancing:
There is no standard way to do that in Blender, but you can create an empty and then parent them all to it. That will place them all inside the empty's listing in the Outliner, out of the way. After creating the empty, just click and drag the objects into it in the Outliner. You should also give the empty a good name to distinguish what it's there for, so you don't have to remember when you come back months later and wonder where all your objects are.