Allogenic Stem Cell Transplantation in Patients With High Risk CD33+ AML/MDS/JMML

Eligibility Inclusion Criteria: Disease Status * AML Induction Failure * AML in 1st, 2nd, or 3rd Relapse (\>10% bone marrow blasts) * AML greater than or equal to 3rd CR * MDS with \>6% bone marrow blasts at diagnosis * Secondary MDS with less than or equal to 5% bone marrow myeloblasts at diagnosis * JMML with \>6% bone marrow myeloblasts at diagnosis Disease Immunophenotype Patients (AML only) receiving gemtuzumab ozogamicin must express minimum of \>10% or =10% CD33 positivity. Patients with \<10% CD33 positivity will not receive gemtuzumab ozogamicin. Organ Function Patients must have adequate organ function as defined below: * Adequate renal function defined as: * Serum creatinine \<1.5 x normal, or * Creatinine clearance or radioisotope GFR 40 ml/min/m2 or \>60 ml/min/1.73 m2 or an equivalent GFR as determined by the institutional normal range * Adequate liver function defined as: * Total bilirubin 1.5 x normal, or SGOT (AST) or SGPT (ALT) \<2.0 x normal or =2.0 x normal * Adequate cardiac function defined as: * Shortening fraction of \>27% by echocardiogram, or * Ejection fraction of \>47% by radionuclide angiogram or echocardiogram * Adequate pulmonary function defined as: * DLCO \>55% or =55% by PFT * For children who are uncooperative, no evidence of dyspnea at rest, no exercise intolerance, and a pulse oximetry \>94% on room air Exclusion Criteria: * Patients with active CNS AML/JMML/MDS disease at time of conditioning therapy * Female patients who are pregnant (positive HCG) * Karnofsky \<50% or Lansky \<50% if 10 years or less * Age \>65 years * Has received gemtuzumab in the previous 30 days or has not recovered from prior gemtuzumab therapy.