My candidate is AA 1562, JFK-PHX, scheduled daily at 09.59 AM:

This is usually a LAA 737 which lands at LGA the night before and goes to the hangar. It is then ferried empty from LGA to JFK in the morning.

The scheduled departure from LGA is 08.00 AM, landing in JFK at 08.40. The morning traffic at LGA between the hours of 7.00 and 9.00 is among the worst in the day, with take off waits over 30 mnts and this has been the case for years.

The plane is overnighting at LGA. There is therefore no problem of incoming flight. One would hope that some high powered brain in the system would think of scheduling the LGA-JFK flight at 07.30 to insure a timely departure from JFK... but no. The same machine usually goes on from Phoenix to Sacramento, unless another plane can be substituted for the late arrival in PHX. From then on, the delays snowball.

Who can believe that the cost of reaccomodating passengers with missed connections ( and this is an almost daily affair...) is less than paying an extra 30 mnts to the crew ferrying the 737 from LGA to JFK ?