The penalty box is just the name that they use. As mentioned, if flights are in ground delay and other planes are waiting to use the gates, they may push back and park in this area so as to free up the gate. Similarly, when planes arrive early at some major airports or a delayed flight is still using the jetway, then the arriving flight is often sent to the penalty box to wait for the jetway to become available. Basically, it is an area that is "out of the way" (not meaning placed in some far off area of the airport) where a plane can park without blocking an active taxiway and inconveniencing other flights. For example, at O'Hare Airport, there is a penalty box just west of United's C concourse between taxiway A4
and A5 or A6. It is a small parking area that planes can pull into and wait so as not to block other aircraft.