Thunderbolts #110-136 - Warren Ellis' examination of Marvel villains was my favorite thing he ever did. For someone who hates super-heroes, his reinvention of Doc Samson, Steel Spider, and especially American Eagle were brilliant. Then Andy Diggle came on board and picked right up and continued the great story.
Invincible Iron Man #1-6 - I adored the opening arc in this series, but it floundered for a bit during the too long Iron Man Disassembled arc. Even at its worst, it is an entertaining book.
Batman #667-669 - Batmen of All Nations - This fantastic story made me realize how much I would have adored Morrison's whole Batman run if there had been a good artist involved. Too bad Tony Daniel was the regular artist.
Hitman #45-49 - This only shipped for 5 months or so in the 2000's, but since it may be my favorite series of all time, it still makes the list.
Beyond! #1-6 & Fantastic Four #544-553 - Dwayne McDuffie cobbled together a classic Marvel U story using all sorts of odd pieces from the Marvel U. He also dusted off the Hood before anyone else did. Scott Kolins on art and a series heavily featuring Hank Pym and the Wasp? That's my perfect storm of a comic. McDuffie and Paul Pelletier picked up some strings from that series and wrote my favorite FF stories. Including the great scene where Black Panther put the Silver Surfer in a headlock!