What do pilots do, when there is a long wait before take-off, after gates are closed?
Apart from what Daniel listed already, they're also nervously watching the clock.
If they're late by too much they may miss their mandatory crew rest period and have to cancel the flight or hand over to another crew.

This can of course get very expensive for the airline, especially if all or most passengers have to be accommodated in hotels overnight for a departure the next day in case no replacement crew can be arranged or the forced delay causes the flight to be unable to take off due to closing of the departure airport before departure or closing of the destination airport before arrival there.