A disclaimer, since I have had to address silly complaints on posts like this before: What I am saying here is that these comics are my personal favorites from this era. I am NOT saying they are objectively the greatest comics of this era. Loosen up and enjoy!
Part 1: Marvel Comics
The New Avengers by Brian Michael Bendis and various artists
This is what made Bendis’s name at Marvel, and this coupled with his runs on Daredevil and related books from the same era likely represent the peak of his comic book work. This book also helped get me back into comics in college after I’d been off the wagon for a short time.
Astonishing X-Men by Joss Whedon and John Cassaday
This comic was a treat, and precedes Whedon’s involvement in The Avengers film by years. It’s sad to think what could have been done if Whedon had had the ability to work with these characters on film as well. I already enjoyed Whedon’s work (Buffy and Firefly, anyone?), so his involvement with another of my favorite properties cinched it for me.
Uncanny X-Force by Rick Remender and Jerome Opeña
When this title was around with Remender at the helm, it was the single best book Marvel was putting out. The choice of cast was spot-on, and they were all handled so very well. In particular, this includes enjoyable versions of both Wolverine and Deadpool, if for any reason you find either character tough to read.
The Amazing Spider-man by J. Michael Straczynksi and various artists
Everybody has a favorite Spider-man storyline/writer, and this one is mine. I’ve read other stuff over the years (the more recent Superior Spider-man being a standout honorable mention), but the full scope of Straczynski’s work on the character and then having all of that undone by a single editorial decision at Marvel grant this period a mythic quality.
The Ultimates and The Ultimates II by Mark Millar and Bryan Hitch
These comics set in a now-dead universe hold a special place in my heart. They provided a well-crafted, action-packed Avengers story in an era that needed it, and it actually held some narrative surprises given the freedoms the Ultimate line afforded. I tell you, these comics had some of the best moments of the entire era, and they accomplished two great feats: 1. They made Captain America a powerhouse badass again, and 2. They presented some ideas that would later be incorporated into the Marvel Cinematic Universe, such as Nick Fury looking like Samuel L. Jackson. Find these and read them if you never have.
Some honorable mentions (besides those mentioned in the post) would include Greg Pak’s run on The Incredible Hulk, Straczynski’s run on Thor, and Fabian Nicieza’s Cable & Deadpool.