Washington Post
The Associated Press and Wall Street Journal can claim they were robbed, says Joel Achenbach. Both did "tremendous work on the gulf oil spill, which was the biggest breaking news story of the year." He goes on:

There are others who might also complain, namely the three finalists in the Breaking News category. The board reportedly couldn’t reach a majority vote (so, um, why not make it a plurality rather than give no award?). ...

I suspect the real problem is that the breaking news category stipulates that the work be “local.” Why make that stipulation? There’s already a separate category for Local News.

David Warsh: Two "extremely strong" series didn't make the Pulitzer finals

Larry Kramer: "If the newspaper industry gives up on breaking news, they should just close their doors"

CORRECTION: This post originally stated that Achenbach was referring to coverage by The Washington Post and the Associated Press, rather than The Wall Street Journal and the AP.