Will, you really shouldn't worry too much about them. They are not taking up that much space and they don't load any applications. They are merely placeholders for data used by other applications.
For instance, the old Bonus Tools' layer command held the data for LayerFilters in the dictionary for the registered app "RAK".
ADT, LDT and other 3rd party app's use these and deleting them will "dumb-down' the drawings as far as those programs are concerned. I just chacked one of my drawings that has been worked on in Softdesk8 and LDT3, it has 42 registered apps, most of which would render the drawing useless, as far as further design goes, if deleted.