This is going to be easy for me considering how few comics I've read so here we go:
Y-the Last Man: This needs to go into the same category as Watchmen and the Dark Knight. It is that good IMO.
The Walking Dead: This series shows that sometimes the humans can be just as bad as the Zombies. Great.
Invincible: Superman mixed with Lee/Ditko Spidey and a drop of Miracleman also. Very much a lighthearted comic book and the best Superhero book on the stands this decade.
New X-Men by Grant Morrison: Say what you want about the end 3/4ths of his run was pretty good. He brought the X-Men into the new millenium and gave them the shot in the arm they needed.
Marvel Civil War: Just to be clear, we're talking about the event as a whole here not the mini-series as that was just a series of vignettes designed to get you to buy the books. But if you did you get a pretty fun and entertaining read.
I'm also probably missing books here as well, but here's a start, in no particular order:
All-Star Superman: Probably the best work that Morrison and Quitely have done to my recollection. And that includes stuff like Flex Mentallo. They managed to hit the core of what Superman is, incorporated the best elements of the mythos, and took it in a distinct direction. More comics need to be like this.
League of Extraordinary Gentlemen: The book that evolved from a Victorian JLA into a detailed mapping of literary history. The sheer number references in this book are simply astounding, and they're all included without dragging down the main action.
Planetary: The ending didn't quite work and the series was incredibly slow, but this was still the one book I always looked forward to most. I'd recommend reading this in collected form.
Green Lantern: This book languished horribly in the 90's, but found a renaissance in the 2000's under Geoff Johns. This run managed to fix all the problems with Hal Jordan, restore the Green Lantern Corps to prominence, make Sinestro a fascinating villain, and create a distinct cosmic landscape in the DCU that we've not seen previously.
52: The weekly comic that defied pretty much all expectations. This book revived a fair number of less prominent characters, and managed to build strong stories for each of them.
Ruse: One of the best books by the late, lamented CrossGen. The early issues by Mark Waid and Butch Guice were among the finest work by both of them, and even Scott Beatty turned in some good locked-door mysteries by the end of the run.
Captain Marvel (Vol. 4): While PAD's run on Captain Marvel was usually at least enjoyable, it was the relaunch that made it stand out. The idea of cosmic awareness driving Genis-Vell into madness was inspired, and brought the book into new heights until its inevitable cancellation.
Punisher by Garth Ennis: The run that singlehandedly revived Frank Castle. While it wasn't quite so golden during most of the Marvel Knights run (with a couple of exceptions), the MAX version of Punisher was riveting for years. Bonus points for giving Punisher classic villains like Nicky Cavella and Barracuda, when the character never had much of a villain roster in the past.
Mark Waid and Mike Wieringo's Fantastic Four: While not a perfect run, this series struck the heart of who the FF were as individuals and as a family. A strong contender for the best FF run since John Byrne's, though admittedly it doesn't have that much real competition.
Seven Soldiers: A grand experiment that very nearly worked except for the ending. Zatanna, Guardian, Frankenstein, and Bulleteer were all great reads on their own, and it was always interesting to find the subtle connections.