Personally, I have the same problem with this category as I do with "best dramatic presentation: short form". I kind of think series should be considered as a whole, with the entire story arc, rather than as individual volumes or episodes, though how well they stand on their own varies and some series are really really long. Hrm. which means they would cross years. That doesn't work either.
Anyway, if anyone cares, my votes for best Graphic Story will likely go as follows:
1. Y: The Last Man, Volume 10 -awesome, and bonus! female artist (Pia Guerra)
2. Girl Genius, Volume 8: Agatha Heterodyne and the Chapel of Bones
3. Fables: War and Pieces
4. Dresden Files: Welcome to the Jungle
5. Serenity: Better Days
6. Schlock Mercenary: The Body Politic
I fear that Serenity: Better Days might win for the nostalgia factor or Dresden Files for the name recognition and the fact that the script is decent even though the graphic story craft is weak in both though worse in Serenity than Dresden Files.