To add to Quizmonster's answer...you'll have seen films where the English redcoats with their muskets are lined up in three ranks against the enemy. The officer in charge shouts out the order, 'Front rank - ready, aim, fire!', and the soldiers loose off a simultaneous volley at the enemy.
The 'Fire at will' command means 'Don't wait for the order to fire a volley, but every man fire individually whenever you want to, and continue to do so until ordered to stop'.
(Of course, there's inevitably some guy named 'Will' who comes in for some stick over the command).