H.A.M.M.E.R. was Norman Osborn's recreation of S.H.I.E.L.D. following the Skrull invasion, retaining only the agents he could trust to be loyal to him instead of Nick Fury and Tony Stark. H.A.M.M.E.R. worked in conjunction with the Dark Avengers and the Thunderbolts Initiative.
(The name H.A.M.M.E.R. was chosen as an aggressive counterpoint to S.H.I.E.L.D., and doesn't actually stand for anything.)