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Top 50 Marvel Comics of the 2000s

There were a few (well at the top of my head, Slott's Amazing Spider-Man, Remender's Punisher, Hickman's Secret Warriors, and Hickman's Fantastic Four) runs where the majority of it and its peaks were in the 2010s despite having a few issues released in 2008/2009 so they have been disqualified. And remember kids, origin stories are stupid!
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Agents of Atlas (Jeff Parker)
Agents of Atlas
1
Jeff Parker
Alias (Brian Michael Bendis and Michael Gaydos.)
Alias
2
Brian Michael Bendis and Michael Gaydos.
Amazing Spider-Man (Straczynski) (J. Michael Straczynski)
Amazing Spider-Man (Straczynski)
3
J. Michael Straczynski
Annihilation (Jeff Vandermeer)
Annihilation
4
Jeff Vandermeer
Annihilation: Conquest
Annihilation: Conquest
5
Astonishing X-Men (Joss Whedon & John Cassidy)
Astonishing X-Men
6
Joss Whedon & John Cassidy
Brian Michael Bendis' Avengers
Brian Michael Bendis' Avengers
7
Stormbreaker: The Saga of Beta Ray Bill (2005) #1 (March 2005)
Stormbreaker: The Saga of Beta Ray Bill (2005) #1
8
March 2005
Cable & Deadpool
Cable & Deadpool
9
Ed Brubaker's Captain America
Ed Brubaker's Captain America
10
Captain Marvel (Peter David)
Captain Marvel
11
Peter David
Civil War (Mark Millar)
Civil War
12
Mark Millar
Daredevil: Brian Michael Bendis Run (Daredevil #26 to #50, #56-81)
Daredevil: Brian Michael Bendis Run
13
Daredevil #26 to #50, #56-81
Daredevil: Ed Brubaker's Run (Daredevil #82 to #119)
Daredevil: Ed Brubaker's Run
14
Daredevil #82 to #119
Exiles #1-#37 (Judd Winick, Mike McKone)
Exiles #1-#37
15
Judd Winick, Mike McKone
Iron Man: Extremis (Warren Ellis)
Iron Man: Extremis
16
Warren Ellis
Fantastic Four (Mark Waid & Mike Wieringo)
Fantastic Four
17
Mark Waid & Mike Wieringo
Guardians of the Galaxy #1-#25 (Dan Abnett, Andy Lanning)
Guardians of the Galaxy #1-#25
18
Dan Abnett, Andy Lanning
House of M (Brian Michael Bendis)
House of M
19
Brian Michael Bendis
Immortal Iron Fist (Matt Fraction)
Immortal Iron Fist
20
Matt Fraction
Incredible Hercules #113-#141 (Greg Pak, Fred Van Lente, Paul Neary)
Incredible Hercules #113-#141
21
Greg Pak, Fred Van Lente, Paul Neary
Invincible Iron Man (#1-33; 500-527) (Matt Fraction & Salvador Larroca)
Invincible Iron Man (#1-33; 500-527)
22
Matt Fraction & Salvador Larroca
The Irredeemable Ant-Man (Robert Kirkman)
The Irredeemable Ant-Man
23
Robert Kirkman
Marvel Knights Spider-Man by Mark Millar (Marvel Knights: Spider-Man #1-12)
Marvel Knights Spider-Man by Mark Millar
24
Marvel Knights: Spider-Man #1-12
X-Men: Messiah Complex (Ed Brubaker)
X-Men: Messiah Complex
25
Ed Brubaker
New X-Men (Grant Morrison)
New X-Men
26
Grant Morrison
Nextwave: Agents of H.A.T.E. (Warren Ellis and Stuart Immonen)
Nextwave: Agents of H.A.T.E.
27
Warren Ellis and Stuart Immonen
Nova (Dan Abnett)
Nova
28
Dan Abnett
Planet Hulk (Incredible Hulk #92-#105) (Greg Pak, Carlo Pagualyan)
Planet Hulk (Incredible Hulk #92-#105)
29
Greg Pak, Carlo Pagualyan
Punisher (Garth Ennis)
Punisher
30
Garth Ennis
Runaways (Brian K.Vaughan)
Runaways
31
Brian K.Vaughan
Secret War (Brian Michael Bendis)
Secret War
32
Brian Michael Bendis
Sentry #1-#5 (Paul Jenkins, Jae Lee)
Sentry #1-#5
33
Paul Jenkins, Jae Lee
Son of M (David Hine)
Son of M
34
David Hine
Supreme Power (2003) (J. Michael Straczynski)
Supreme Power (2003)
35
J. Michael Straczynski
Thor (J. Michael Straczynski)
Thor
36
J. Michael Straczynski
Thunderbolts (Warren Ellis)
Thunderbolts
37
Warren Ellis
Ultimate Galactus Trilogy (Warren Ellis)
Ultimate Galactus Trilogy
38
Warren Ellis
Ultimate Spider-Man
Ultimate Spider-Man
39
Ultimate X-Men
Ultimate X-Men
40
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