Well the jump seat can be used for two things:
1. If a pilot has to get a transfer from where he lives to the hub he (or she) could ride in the jump seat for the flight. (Example say a pilot lives near KSFO, but his hub is in KJFK, he could ride in the jump seat on a KSFO-KJFK flight and the fly his routes (I'm almost positive lou has done  something similar to this quite a few times))

2. If a 757 or 767 or most other planes are flying a long routes there will often be another F/O or Captain in the jump seat so the pilots can switch out as they get tired mid-flight.