The Beat has the whole list of winners here.
Some of the notable ones for me:
Batman / Spirit #1 (Cooke & Loeb) - best issue.
(Ironic following the announcement that Cooke & Bone are leaving after #12. That's the Spirit revival dead in the water then.)
All Star Superman - best continuing series.
Criminal - best new series.
Left Bank Gang - best US edition of international material.
Paul Pope - best writer/artist (Batman:Year 100).
Hope Larson - special recognition (Grey Horses).