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 specific weapon types used in the HAMMERDOWN protocol included Mk-82 general purpose bombs, 80 of which were dropped in one specific bombing run by a B-2 Spirit.  It is also widely believed that Massive Ordnance Air Blast bomb's (M.O.A.B.) were deployed against the LSA when the bombing runs after the protocol was initiated. It is highly unlikely any sort of Nuclear Weapon was used, as their lasting radiation effects would be an unwanted aftermath.
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.