From all that I read during 2000-2009, these are my favorite books - ongoing titles, minis, one-shots, collections, OGNs, back issues, super hero or otherwise. Note that word read. They needn't have been brand-new at the time I found them.
MY FAVORITE ONGOING SERIES (SUPER HERO): Incredible Hercules by Greg Pak & Fred Van Lente.
There were a number of ongoing titles I followed this last decade which I would consider great comics (see below), but above them all I've chosen Incredible Hercules. Although it hasn't approached the epic level of Pak's previous work on Incredible Hulk, it makes fine use of the Marvel Universe and Greek mythology while mapping out its own directions. It's often very funny, occasionally poignant. The recent in-story references to Joseph Campbell point to the series as the journey of a modern-day hero and the gradual development of Amadeus Cho from know-it-all novice to responsible hero has been entertaining to watch.
Also of Note: Agents of Atlas, Amazing Spider-Man, Astro City, Atomic Robo, Avengers: The Initiative, Black Panther (by Priest), Blue Beetle (by John Rogers), Cable/Deadpool, Detective Comics (by Paul Dini), Dynamo 5, Fantastic Four (by Mark Waid), Guardians of the Galaxy, Immortal Iron Fist (by Matt Fraction), Incredible Hulk (by Greg Pak), Invincible Iron Man, Nova, Runaways (by Brian K. Vaughn), She-Hulk (by Dan Slott), Spider-Girl, Thunderbolts (by Fabian Nicieza)
MY FAVORITE ONGOING SERIES (NON-SUPER HERO): Rex Libris by James Turner.
Rex Libris was the book for me, merging the world of librarians with action and laughs...mostly laughs. The librarian action hero concept caught my attention, but the consistently fun situations and high-brow jokes held me there.
Also of Note: Comic Book Comics, Fell, Johnny Hiro, North World, Planetary, Proof, Scott Pilgrim, Street Angel, the Unwritten, Warlord of Io
MY FAVORITE MINI-SERIES/ONE-SHOT (SUPER HERO): Agents of Atlas by Jeff Parker and Leonard Kirk.
As much as I loved the old What If story "What if the Avengers Had Been Formed in the 1905s," I wouldn't have guessed that it could make for a brilliant new star in Marvel's universe. Jeff Parker placed his stamp on these mostly-forgotten characters and the combination of espionage, action and laughs in the original mini-series made for a thoroughly excellent super hero story. I would have been entirely pleased with Agents of Atlas even if the mini-series were all that existed, but the succeeding ongoing format was an additional pleasure.
Also of Note: Annihilation, Chamber, Empire, GLA, Gravity, the Hood, Iron Man: Hypervelocity, Livewires, Seaguy, Spider-Man/Human Torch, Suicide Squad: Raise the Flag, Umbrella Academy, War of Kings, Wednesday Comics
MY FAVORITE MINI-SERIES/ONE-SHOT (NON-SUPER HERO): Global Frequency by Warren Ellis.
I felt that the decision to change artists for each installment of this twelve-issue series was little more than a gimmick. Some great artists graced this series and the particular format of rotating stars in each self-contained issue lent itself to that set-up, but what interested me were the stories, not the art. Global Frequency had a great concept and made the most of it; drawing mostly-normal people into mostly sci-fi threats paid off time and again, my favorite being the issue with the bionic man. This was also a turning point for me in terms of learning to appreciate Warren Ellis, a writer I hadn't thought much of previously.
Also of Note: Arrowsmith, Beasts of Burden, BPRD: the Ectoplasmic Man, the Muppet Show, Mysterius the Unfathomable, Potter's Field
MY FAVORITE SERIES WHICH ENDED ALL TOO SOON: Street Angel by Jim Rugg.
Well, I'd like some more Rex Libris too, but I was served 13 helpings of that series; Street Angel only made it to six issues. Street Angel brought me in to the black & white independent books and I was immediately taken with its humourous reworkings of cliches, particularly the running gags about ninjas. It also brought Jim Rugg to my attention and I've enjoyed his work in other places since then. More, please?
Also of Note: Agent X, El Cazador, Johnny Hiro, Sentinel, Storm Shadow
MY FAVORITE MARVEL SERIES THAT WAS MOSTLY IGNORED: Thanos by Keith Giffen.
Giffen did continue some of his ideas for Thanos into the first Annihilation event, but the series itself had a fun take on Thanos similar to Priest's Black Panther in that Thanos' motivations and inner thoughts were hidden from the readers, leading to great payoffs when the pieces fell in place. It seems to me that Thanos the wandering pilgrim of the cosmos is the perfect place to take the character, given that Jim Starlin made him unsuitable as a villain.
Also of Note: the Crew (by Priest), Exiles (by Jeff Parker), Inhumans (by Sean McKeever), Iron Man (by John Jackson Miller), Master of Kung Fu (by Doug Moench), True Believers, X-Factor (by Jeff Jensen)
MY FAVORITE TRADE PAPERBACK/COLLECTION: Nick Fury, Agent of SHIELD by Jim Steranko.
My trade paperback collection exploded across 2000-2009, but my absolute favorite is one of the earlier ones I purchased that decade: the collection of Jim Steranko's Nick Fury stories from Strange Tales. Partly this is because I enjoy the stories so much; partly it's because of the reproduction efforts and extras; partly it's to see Steranko's 4-page splashes finally shown the way they were intended. Mostly, it's because this is one trade paperback I go back to read for pleasure again and again.
Also of Note: 300, Action Philosophers!, Agents of Atlas, Al Williamson's Flash Gordon, Batman: Year One, Batman: Year 100, Blazing Combat, Dan Dare, Dr. 13: Architecture & Mortality, Golgo 13, Invincible, Johnny Hiro, Judgment Day, Marvels, Masterpiece Comics, Maus, the Nearly Complete Essential Hembeck Archives Omnibus, Ocean, the Rocketeer: the Complete Collection, Shockrockets, Showcase Presents Bat Lash, Showcase Presents Shazam!, Street Angel, Superman: Whatever Happened to the Man of Tomorrow?, Supreme, V for Vendetta, Watchmen, Zot!: the Complete Black & White Collection
MY FAVORITE ORIGINAL GRAPHIC NOVEL: The Interman by Jeff Parker.
It's good to go into a book without any expectations some times. I knew Parker's abilities as a writer from Agents of Atlas, but I knew nothing about his strengths as an artist. This fast-moving espionage story works because Parker developed an action hero who is simply relatable; superhuman in his abilities but human in his reactions to dangerous situations. The Interman sidesteps so many cliches of the action hero and questions everything from the evil twin to the murderous hero.
Also of Note: Bookhunter, It Rhymes With Lust, Midnight Sun, the New Adventures of Abraham Lincoln, Pride of Baghdad, Understanding Comics, a Wizard's Tale
MY FAVORITE BACK ISSUES: Suicide Squad by John Ostrander.
I've always been very strong on my Marvel back issues, but it wasn't until my income increased that I began digging up older books from other companies which had interested me. The concept of Suicide Squad had always fascinated me; how wonderful to discover that the series itself was so good! From the civilian support crew who kept the Squad ready for field work, to the tarnished heroes, to the unrepentant criminals who made up the Squad, Suicide Squad told interesting tales of the Cold War, drawing on actual events for inspiration. Unbelievable as the DC super hero universe is, Suicide Squad captures a sense of verisimilitude; it's a world where Darkseid can raise the dead, but also a world where a lonely computer technician can be shot in the back and a self-serving lowlife can outlive scores of people better than him.
Also of Note: 1963, Astro City, Deadshot (by John Ostrander), Destroy!, Eclipse Magazine, Firestorm (by John Ostrander), Lobo (by Keith Giffen), Manhunter (by John Ostrander), OMAC (by John Byrne), Quantum & Woody (by Priest), Red Rocket 7, Weirdworld, Youngblood (by Alan Moore)
MY SINGLE FAVORITE ISSUE: Astro City: Samaritan Special#1 by Kurt Busiek & Brent Anderson.
This was the story of the Superman-like hero Samaritan and his nemesis Infidel. The duo are so evenly-matched that neither one can entirely defeat the other. Consequently, they call a truce once each year and share a dinner, but spend that dinner scanning each other, looking for a sign of weakness that might tip the balance to their favour. If anyone doubts that Kurt Busiek's Astro City lacks the punch it had in the 1990s, this is the best antidote to that kind of thinking.
Also of Note: Action Comics#775, Astro City: Local Heroes#2, Atomic Robo & Friends FCBD Edition, Deadpool#67, Fantastic Four#60, Marvel Adventures Avengers#12, Marvel Adventures Fantastic Four#12, Peter Parker: Spider-Man#35, Peter Parker: Spider-Man#37, Solo#11, Young Allies Comics 70th Anniversary Special#1
MY FAVORITE BOOK I CONTRIBUTED TO: Marvel Mystery Comics Handbook 70th Anniversary Special by Michael Hoskin.
I wrote or co-wrote a lot of comics last decade, but this one was particularly important to me. It wasn't as widely-read as I would have liked, but I'm so happy that I was able to bring dozens of Marvel characters from the first year of the company's publication back into the spotlight, ever so briefly. It's also a pleasure to have new artwork whenever possible and Gus Vazquez turned in some sharp work.
Also of Note: All-New Iron Manual, Annihilation: Nova Corps Files, Annihilation Saga, Dark Reign Files, Marvel Atlas, Marvel Monsters: From the Files of Ulysses Bloodstone, Marvel Pets Handbook, Marvel Westerns: Outlaw Files, Official Handbook of the Marvel Universe: Golden Age 2004, War of Kings Saga