The one that started it all: the crossover before there were crossovers. Not a great artistic success, but a fantastic commercial one.

You can see where it fits into the larger timeline here.

Harbingers:
X-Men #178 Marvel Masterworks: The Uncanny X-Men. vol.10
Uncanny X-Men Omnibus, vol.4
Essential X-Men, vol.4
Departures
Iron Man #181 Iron Man Epic Collection vol.11: Duel of Iron
Captain America #292 Captain America: Death of the Red Skull
Captain America Epic Collection, vol.11: Sturm Und Drang
Thor #341 (pp1-2) [1] Marvel Masterworks: The Mighty Thor, vol.23
Thor by Walter Simonson, vol.1
Thor by Walter Simonson Omnibus
Avengers #242 Avengers: Absolute Vision Book 2
Thor #342 (bonus panels only) [1] Marvel Masterworks: The Mighty Thor, vol.23
Thor by Walter Simonson, vol.1
Thor by Walter Simonson Omnibus
X-Men #179 Marvel Masterworks: The Uncanny X-Men. vol.10
Uncanny X-Men Omnibus, vol.4
Essential X-Men, vol.4
Peter Parker, The Spectacular Spider-Man #89 [2] Marvel Masterworks: The Spectacular Spider-Man, vol.7
Essential Peter Parker: The Spectacular Spider-Man, vol.4
Marvel Team-Up #140 [2] un-collected
Amazing Spider-Man #251 [2] Marvel Masterworks: Amazing Spider-Man, vol.23
Spider-Man: Origin of the Hobgoblin
Spider-Man by Roger Stern Omnibus
Incredible Hulk #294 Incredible Hulk: Regression
Fantastic Four #264 Fantastic Four by John Byrne Omnibus, vol.2
Fantastic Four Visionaries – John Byrne, vol.4
The Thing #10 The Thing Classic, vol.1
The Thing Omnibus
The Secret War
Secret Wars #1 Secret Wars Omnibus
Spider-Man & The Secret Wars
Deadpool’s Secret Secret Wars
“Whatever Happened to Master Blood” in Spider-Man: Black Suit and Blood #3 [tk] Spider-Man: Black Suit and Blood
Secret Wars #2 Secret Wars Omnibus
Secret Wars #3 Secret Wars Omnibus
She-Hulk #10 [3] Secret Wars Omnibus
She-Hulk, vol.2: Superhuman Law
She-Hulk by Dan Slott Omnibus
Thor #383 [4] Secret Wars Omnibus
Thor Epic Collection, vol.16: War of the Pantheons
Secret Wars #4 Secret Wars Omnibus
Spider-Man and the Secret Wars #1 [5] Spider-Man & The Secret Wars
Secret Wars #5 Secret Wars Omnibus
Secret Wars #6 Secret Wars Omnibus
Spider-Man and the Secret Wars #2 [6] Spider-Man & The Secret Wars
Secret Wars #7 Secret Wars Omnibus
Secret Wars #8 Secret Wars Omnibus
Spider-Man: Birth of Venom
Secret Wars #9 Secret Wars Omnibus
Spider-Man and the Secret Wars #3 [7] Spider-Man & The Secret Wars
Secret Wars #10 Secret Wars Omnibus
Spider-Man and the Secret Wars #4 [8] Spider-Man & The Secret Wars
Secret Wars #11 Secret Wars Omnibus
Secret Wars #12 Secret Wars Omnibus
Secret Wars: Battleworld #1 [9] Secret Wars: Battleworld
Secret Wars: Battleworld #2 [9]
Secret Wars: Battleworld #3 [9] Secret Wars: Battleworld
Secret Wars: Battleworld #4 [9] Secret Wars: Battleworld
Returns and Epilogues
Deadpool’s Secret Secret Wars #1 [K] Deadpool’s Secret Secret Wars
Deadpool’s Secret Secret Wars #2 [K] Deadpool’s Secret Secret Wars
Deadpool’s Secret Secret Wars #3 [K] Deadpool’s Secret Secret Wars
Deadpool’s Secret Secret Wars #4 [K] Deadpool’s Secret Secret Wars
Avengers #243 [11] Avengers: Absolute Vision Book 2
Iron Man #182 [11] Iron Man Epic Collection vol.11: Duel of Iron
Iron Man #183 [12] Iron Man Epic Collection vol.11: Duel of Iron
Thor #341 (p3 onwards) [1] Marvel Masterworks: The Mighty Thor, vol.23
Thor by Walter Simonson, vol.1
Thor by Walter Simonson Omnibus
Amazing Spider-Man #252 [2] Marvel Masterworks: Amazing Spider-Man, vol.24
Spider-Man: Birth of Venom
Spider-Man: The Complete Alien Costume Saga Book 1
Spider-Man: The Complete Black Costume Saga Omnibus
Marvel Team-Up #141 [2] Spider-Man: The Complete Alien Costume Saga Book 1
Spider-Man: The Complete Black Costume Saga Omnibus
Peter Parker, The Spectacular Spider-Man #90 [2] Marvel Masterworks: The Spectacular Spider-Man, vol.7
Essential Peter Parker: The Spectacular Spider-Man, vol.4
Spider-Man: The Complete Alien Costume Saga Book 1
Spider-Man: The Complete Black Costume Saga Omnibus
X-Men #180 Marvel Masterworks: The Uncanny X-Men. vol.10
Uncanny X-Men Omnibus, vol.4
Essential X-Men, vol.5
X-Men #181 Marvel Masterworks: The Uncanny X-Men. vol.10
Uncanny X-Men Omnibus, vol.4
Essential X-Men, vol.5
X-Men #182 [13] Marvel Masterworks: The Uncanny X-Men. vol.10
Uncanny X-Men Omnibus, vol.4
Essential X-Men, vol.5
Incredible Hulk #295 Incredible Hulk: Regression
Fantastic Four #265 Fantastic Four by John Byrne Omnibus, vol.2
Fantastic Four Visionaries – John Byrne, vol.4
Marvels: Eye of the Camera #4 Marvels: Eye of the Camera
The Thing #11 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #12 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #13 [13] The Thing Classic, vol.2
The Thing Omnibus
The Thing #14 [13] The Thing Classic, vol.2
The Thing Omnibus
The Thing #15 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #16 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #17 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #18 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #19 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #20 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #21 [14] The Thing Classic, vol.2
The Thing Omnibus
The Thing #22 [14] The Thing Classic, vol.2
The Thing Omnibus
Fantastic Four #274 [15] The Thing Classic, vol.2
The Thing Omnibus
Fantastic Four Visionaries – John Byrne, vol.5
Fantastic Four by John Byrne Omnibus, vol.2
Spider-Man: Birth of Venom
Quasar #8 [16] Quasar Classic, vol.1
Secret Wars II Omnibus

Footnotes:

  1. The entirety of Secret Wars takes place between pages 2 & 3 of Thor #341. In #341, there were three whited out panels – panels which were provided the following month in the letter column of #342.
  2. These two sets of three issues all happen at around the same time.
  3. This story depicts an expanded version of the origin of Titania seen in Secret Wars #3.
  4. The vast majority of this issue takes place at this point.
  5. Takes place entirely within Secret Wars #4
  6. Appears to take place around the time of Secret Wars #6
  7. Jumps around a bit chronologically, but after Secret Wars #9 is the best fit.
  8. Takes place entirely within Secret Wars #10
  9. Takes place entirely between panels 4 & 5 on page 36 of Secret Wars #12, according to editorial notes in the story.
  10. Tells various incidents across the whole span of the original series, but best read here to avoid spoilers.
  11. Iron Man returns with the Avengers.
  12. Iron Man deals with some fallout from the Secret Wars.
  13. An epilogue, but probably the single best issue of the whole storyline.
  14. The Thing remained on Battleworld for 12 issues of his own title before returning to Earth.
  15. The Thing finally returned to Earth in this issue.
  16. Quasar deals with some fallout from Iron Man’s fallout, above.