It also makes a difference on AA/Eagle/Connection for parents of employees if they are traveling with the employee. Unaccompanied parents are D2P priority (and below all ordinary D2s regardless of check in time), but your parents are traveling with you, they can then be ordinary D2s.

Also any nonrev passenger who is transiting a city is automatically moved up ahead of passengers originating in that city (D2T ahead of D2, etc). So a pilot commuting MIA-ATL will always be below, for example, a spouse of another employee who went EYW-MIA-ATL using a D1 (but as was mentioned before, there's still the jumpseat)