The ones that come to mind are the MD-80 flights to ROW. Typically flight numbers that are west bound are odd numbers whereas those east bound are even numbers. However when AA has flown MD-80s on a single leg from DFW to ROW, it has interchanged odd and even flight numbers. For example AAL 9612 and AAL 9631 both were MD-80 flights to their probable final resting place at ROW. Similar odd and even flight numbers have been used also from STL to ROW and ORD to ROW, probably because these flights are non-passenger flights. :-:

I do have an unusual story to tell about TWA and a flight number. One day I noted I was on TW flight 003 from STL to LAX and the plane number was 11003, a three engined Lockheed Tristar. I then looked at my boarding pass, and I was seated in 3-1, and it was 3/3. Flight 003 had been subject to a variety of superstitions ever since Carole Lombard boaded a DC-3 from Las Vegas to LAX, but the plane crashed under mysterious circumstances. I remember reading about some of these superstitious comments that were described in one of the books on the history of TWA attesting to the frequent occurence of 3s that occured on this fatal crash.
After arriving safely at home, I sent an email to TWA management recounting the infamous DC 3 flight TW 003, and how Clark Gable,waiting at LAX to meet his wife, heard of the tragedy. Needless to say, the next time I was on a flight leaving at the same time from STL to LAX, the flight number had been changed!