The voting breakdown for the 2009 Hugo Awards is available here.
Novel (936 ballots): In the end it really was between The Graveyard Book and Anathem, but when it came to the runoff for second place, Little Brother ranked over Anathem.
I've seen Kevin Standlee explain this before, but it takes a while for the math to sink in. I believe the winner has to have the majority of all votes cast and if that doesn't happen in the first round, the work with the lowest votes is dropped, the votes are redistributed, and it repeats until there is a winner. Something like that. This allows the winners to be more of a consensus pick, the work that most of the ballots felt was the strongest rather than necessarily being the work the most people gave first place votes to in the first round.
Novella (696 ballots): Like the novel category, "The Erdmann Nexus" won over "The Tear", but then "Truth" won the runoff for second place.
Novelette (760 ballots)
Short Story (826 ballots)
Campbell (431 ballots): While Durham led for all rounds of calculating (with a 16 vote margin in the first round), by the end he won by only three votes over Aliette de Bodard. Phew!
In all five categories I listed above, all the winners led for all five rounds of calculations. This was the case in MOST of the categories. Semiprozine is a glaring exception to this as Locus had the most first place votes and the eventual winners, Weird Tales, had the third highest total of first place votes.