I love the fact that Cipher doesn't have the girl that was introduced at the start as the heroine, but the twins are the heroes ^^. It has a satisfying ending, as well (but that one utter over the top bit - the car accident... really could have been taken out ).

1) xxxHolic - the crack recommended by Melinda that started this all for me.
2)Fruits Basket - this series has such a warm and cozy place in my heart
3)Bleach

Oh so hard to choose! I considered listing Tsubasa: Reservoir Chronicles as tied with xxxHolic. The series really grabbed hold of me with volume 16 and since its story is irrevocably intertwined with that of xxxHolic, I really cannot consider my love for one without the other. I also agonized over including Fullmetal Alchemist, which if you ask me tomorrow I'll wish I had put in place of Bleach.

NEW
1) Maka Maka - I don't care, it's gorgeous and moving and the world would be a better place if we had more yuri that didn't look it was conceived by a 13 year old male
2) Me and the Devil Blues - too intriguing to pass up
3) Cat-Eyed Boy - haven't read vol 2 yet, but 1 is creepily delicious

CONTINUING
1) Monster - I haven't finished it yet, so it may yet fall apart (see #3 below), but I love it as much for the smaller moments and one-off chapters as for the main story
2) Berserk - I'm waaaaay behind on this one, but it's always managed to fulfill both my barbaric and court intrigue joneses
3) Death Note - I actually thought the end worked okay, but some of the second half's "twists" were pretty lame. I think it has to go on here as a watershed in manga considering how much it crossed over into the greater US comics and sci-fi/fantasy markets

New:
1. Nabari no Ou
2. High School Debut
3. Ummm... Those two are really the only new ones I've read and enjoyed.

For best continuing, though:

1. xxxHolic
2. D. Gray-man (I will second Elena's lonely recommendation, lol. D. Gray-man is absolutely amazing and needs more love)
3. Bleach (I can't help it; I love it)

Best new:
High School Debut
Kiichi and the Magic Books
Silver Diamond

- all the other ones I came up with (ZigZag, Hibiki's Magic)started with their first volumes last November or December, oh well.

Continuing:
Cipher (ended)
Emma
Aria

I'd put Fruits Basket here, too, but that's already been mentioned enough.

New:

1) Real
2) Me and the Devil Blues

Continuing:

1) Kurosagi Corpse Delivery Service
2) Death Note (Well, sorta)

Real - Takehiko Inoue

Continuing

Vagabond- Takehiko Inoue

Indeed.

Best New:
Black Jack
High School Debut
Sand Chronicles

Best Continuing:
NANA
Vagabond
Tail of the Moon

Best New:

Sand Chronicles
High School Debut
Honey & Clover

(We Were There also looks really promising, but I haven't read the second volume yet.)

Best Continuing:

Fruits Basket
NANA
...and I'm going to go with xxxHOLiC for my third, but there're a lot of contenders (Ouran, ASN, Kurosagi, FMA, Monster...). Furuba and NANA were no-brainers for me, though. I'm madly in love with both of them. ^_^

Erin: I considered Hikaru no Go on my list too, but I kind of hate the extreme Americanization of the Viz editions. Am I being too harsh?

Honey & Clover

and ... err ... man, I didn't read too much in the way of new (or "new") manga this year. But ...

Best ongoing:

Excel Saga (criminally underrated, underdiscussed, underread ...)
Monster
One Piece

GO Naruto
NARUTO#!