Some favourites of mine:

Scott Pilgrim - great comic or greatest comic?
Street Angel - oh man, I wish there was more of this
Death Note - needed a few more coincidences
Fell - hope Warren and Ben continue this
Casanova - hope this continues too
Desolation Jones - and this too, heh
Concrete - gotta love Concrete, dontcha?
Nextwave! - too good to be Marvel
Criminal - why aren't there more crime comics?
Sleeper - dark, dark, dark. Love it
Incognito - kind of like Sleeper Lite
From Hell - I always knew the Stone Cutters were Jack the Ripper
V for Vendetta - yay for anarchy
Watchmen - better than you imagine
League of Extraordinary Gentlemen - I gotta read all of this
The Drifting Classroom - Lord of the Flies on crack and meth
The Winter Men - way too short, I want moar
DMZ - the hipsters will inherit the earth
Local - who doesn't hate Megan?
Action Philosophers - most education I've ever got
Comic Book Comics - why hasn't there been something like this before?
The Push Man and other stories - Tatsumi-sensei is the man
Abandon the Old in Tokyo - is this the one with the dog story? shudder
Goodbye - I love Tatsumi's disturbing little short stories
A Drifting Life - Epic Yoshiro Tatsumi. Can't wait for part 2
Dragon Head - gotta read the rest of this
Oldboy - the movie was actually kind of better
The Kurosagi Corpse Delivery Service - each friggin' chapter of this could be its own series
Mail - same as Kursagi
Sin City - this is the one that dragged me back into comics
Queen and Country - I've really gotta read the rest of this
Dark Mists - geisha spies. Not much action but I liked it for some reason
The Escapists - anyone who ever wanted to create something should read this
Y: The Last Man - got kind of bored with this. Have to read the rest
Empire - Dr Doom takes over the world
Yotsuba&! - w00t. Gotta love Yotsuba
Planetes - I really wish there was more astronaut fiction
Polly and the Pirates - where are her feet?
Hellboy and BPRD - ya, I got dragged into these
The Goon - it's awesome, isn't it
Usagi Yojimbo - Stan Sakai is a frikking amazing cartoonist, isn't he?
Fear Agent - get back on this, Remender.
Umbrella Academy - hard to believe this is good
Scalped - so sleazy
Elephantmen - Mappo is my family
The Secret Voice - where the hell is issue 2?
The Killer - the French can sometimes make good comics
The Punisher (Garth Ennis) - it was pretty sweet
Wasteland - can't wait to find out what the big wet was
The Pirates of Coney Island - stab stab stab
Agents of Atlas - Jeff Parker is a god
Wormwood Gentleman Corpse - he's a funny little worm
The Black Coat - I love characters who have a network of agents
Black Gas - it was all right
Black Harvest - this too
Black Metal - m/
Black Summer - super hero decadence at its finest
Black Hole - so good, so creepy
The Boys - meh, I liked it for some reason
The Other Side - the was a pretty amazing little series, wasn't it
Negative Burn - I love short stories. I should read more
The Nightly News - pretty hardcore
Transhuman - gotta get a can-hand
Pax Romana - I hope this happens some day
Phonogram - I recognize about 1% of the music references
Suburban Glamour - yay, fairies
Cromartie High School - so funny, gotta get the rest
BLAME! - I think about this one a lot but I've only got the first 2 volumes
Mouse Guard -
Okko
JTHM and Squee!
Box Office Poison
Jimmy Corrigan
Battle Royale
Blankets
Tokyo Babylon
The Losers
Sexy Voice and Robo
Oribter
Apparat
Scars
Global Frequency
Transmet
The Authority
Gravel
Anna Mercury
No Hero
Doktor Sleepless
Switchblade Honey
Freakangels
Ignition City
Preacher
Godland
Capote in Kansas
American Born Chinese
Bone
Invincible
FLCL
Lost at Sea
Tanpenshu
King City
Burma Chronicles
Pyongyang
Shenzhen
The Middlesex County Trilogy
Tekkon Kinkreet
Louis Riel
Super Spy
Disappearance Diary
Too Kool To Be Forgotten
Whiteout
Parasyte
Me and the Devil Blues
Mushishi
Maus
solanin
Crossed
Three Shadows
Sulk
Capacity
Black Jack
That Salty Air
Fox Bunny Funny
Pluto
20th Century Boys
North World
Elk's Run
Crogan's Vengeance
Less Than Heroes
Sayonara, Zetsubou-sensei
Mesmo Delivery