Killzone 2 is beating every other shooter in NeoGAF's GotY voting thread. As of the first ten pages, it's leading its closest competitor, Modern Warfare 2, 144 votes to 92.
I doubt too many websites aside from GameSpot and all the PlayStationWhatever.coms will give it the credit it deserves, though. Call of Duty is what's popular, and Call of Duty is what'll get them hits.
Edit:
Counted some more. As of page 15, Killzone 2 has 227 votes, while Modern Warfare 2 has 131.