HAMMERDOWN was the codename for an air strike used in a last ditch effort to destroy the Large Scale Aggressor (LSA)/Cloverfield Monster and the Human Sized Parasites (HSPs)/Parasites, resulting in the destruction of Manhattan itself. The protocol was approved by the United States government at 0442 (4:42am) hours. 120 Minutes later (6:42am), the HAMMERDOWN protocol was initiated.  It was possibly dropped by either a B-52 Stratofortress or a B-2 Spirit.
The "Hammerdown Protocol" appears to be a scorched-earth tactic, officially declaring a United States city a complete loss, and authorizing its wholesale destruction by use of any and all ordinance, to contain a threat rather than let it spread to the rest of the country.
The specific weapon types used in the HAMMERDOWN protocol are unknown, but Mk-82 general purpose bombs were used previous to it, 80 of which were dropped in one specific bombing run by a B-2 Spirit. 
The "Investigation Mode" feature on the Blu-ray release of Cloverfield notes that HAMMER-DOWN used "significantly heavier ordinance" than that witnessed by Hud from the evacuation helicopter, which were the Mk-80 bombs dropped by a B-2 Spirit mentioned above.  
Possible Weapon Types
- The Hammerdown protocol was referenced in the game Call of Duty: Modern Warfare 2. In the game, the player, during an invasion of Washington, D.C. by Russian military, must reach the White House to signal the air force not to go ahead with the Hammerdown intended to destroy the city and stop the Russian advance. Its use was intended as a Cloverfield reference.