Defabricator

The defabricator was a device from the year 200,100. It was previously used by the Trin-e and Zu-Zana robots on the series upgraded version of "What Not to Wear" from the 21st century. Its original use was to "defabricate" clothing by making it literally disappear. Captain Jack Harkness was able to upgrade the device into a powerful weapon, by tweaking the system, after he destroyed the robots, who tried to kill him. The weapon fired a bluish beam of energy that was capable of piercing Dalekanium armour, hence can destroy a Dalek. During the Battle of the Game Station, Jack killed a Dalek with it, but resulted in depleting the power source. (DW: Bad Wolf / The Parting of the Ways)

Jack had somehow managed to have brought this weapon along with him and used the weapon again when the Earth was stolen by the Daleks. Apparently this time he had replaced the power source with a better one as he was able to use it at least twice: killing a Dalek and the Supreme Dalek. (DW: The Stolen Earth / Journey's End) It was presumably destroyed when the British Government destroyed Torchwood Three's base during the 456 incident. (TW: Day One (Children of Earth))

It's likely Jack recovered the defabricator after the events of DW:Last of the Time Lords'', because the weapon was presumingly left on the TARDIS after Jack used it against a Dalek, and it was only after the Master's defeat that Jack would have had an opputunity to recover it (although he wasn't seen with it when he left to go back to his team, which either meant that he dropped it off somewhere to collect first or asked the Doctor to drop it somewhere for him). Alternatively, seeing, Jack's good knowledge on how to mofify the device (as seen when he upgrades it after destroying Trin-e and Zu-Zana) means that it is possible that he buillt this one from scratch.''