Bit late, but:
Full Metal Alchemist.
It's been consistently good all year. I could point to all 12 chapters of 2009 and be happy with them.
By comparison, every other manga I like has had highs and lows. Nothing consistent. One Piece had a good prison, but a poor war. Naruto had a good meeting, but too much emo. lolbleach. Fairy Tail had a dragged out arc, but was consistent in its average-good rating.
The other mangas I either don't read (everything else in the poll), or weren't spectacular (Negima, Ippo, Air Gear, To-LoveRU).
I picked up some mangas this year which I've enjoyed a lot, but upon looking back they haven't had "good" years, it's just that I've caught up (Soul Eater, Kekkaishi, Reborn)