UA operates the Island Hopper, UA 154, which flies HNL-MAJ-KWA-KSA-PNI-TKK-GUM (UA 155 is the return).

DL also recently scrapped their plan to fly JHB-CPT-ATL as a direct flight.

Not aware of any direct with a stop flights on AA, although you'd think they'd be of some use for routes to/from DCA and LGA given the perimeter restrictions.