Doctor Doom chronology

PRE-FIRST-APPEARANCE RETCONS
Invaders #32-33
Marvel Universe #2
Before the Fantastic Four: Reed Richards 1-3

AND NOW STARTING WITH HIS FIRST APPEARANCE
Fantastic Four (1961) #5-6
Fantastic Four 10
Fantastic Four 16-17
Amazing Spider-Man (1963) #5
Avengers 1 1/2
X-Men/Dr. Doom '98
Fantastic Four 23
Fantastic Four Annual #2 (3rd story, then 1st story)
Spider-Man/Human Torch #1
Fantastic Four #39-40
Fantastic Four #43
Fantastic Four Annual #3 ~ Marvel Heroes & Legends '96
Avengers #24-25
Spider-Man and the Fantastic Four (2010) #1
Fantastic Four #56-60
Silver Surfer: Loftier Than Mortals #1-2
Strange Tales #161-167 (Nick Fury stories only, mostly behind the scenes)
Daredevil #36-38
Marvel Super-Heroes #20
Fantastic Four 84-87
Sub-Mariner #20
Fantastic Four: The World's Greatest Comic Magazine #1-12
Astonishing Tales #1-5
Incredible Hulk #143-144
Astonishing Tales #6-8
Fantastic Four #116
Sub-Mariner #47-49
Thor #182-183
Luke Cage, Hero for Hire #8-9
Fantastic Four #143-144
Giant-Size Super-Villain Team-Up #1 (part reprint)
The Iron Age #2 (2nd story)
Fantastic Four #155-157
Super-Villain Team-Up 1-4
Marvel Team-Up 42-44
Super-Villain Team-Up 5-9
Avengers #155-156
Super-Villain Team-Up 10-12
Marvel Comics Super Special #1 (KISS)
Super-Villain Team-Up 13-14
Champions #16
Master of Kung Fu 59-60
Thor #271
Fantastic Four #193-200
Fantastic Four Annual #15 (2nd story)
Amazing Spider-Man Annual #14
Uncanny X-Men #145-147
Dazzler #3-4
Iron Man #149-150
Fantastic Four #236-237
Micronauts #41
Fantastic Four #246-247
Fantastic Four #258-260
Fantastic Four #267-268
Fantastic Four #278-279
Fantastic Four #287-288
Marvel Super Heroes Secret Wars 1-12
1985 #1
Secret Wars II #7
Marvel Graphic Novel: Emperor Doom
Cloak and Dagger (1985) #9-10
Fantastic Four #300
Fantastic Four Vs. X-Men #1-4 (doesn't appear in #1)
X-Factor Annual #4 (2nd story)
Fantastic Four #305
Fantastic Four Annual #20
Fantastic Four #311-312
Damage Control #2
Fantastic Four Annual #21 (2nd story)
Fantastic Four #318-320
Incredible Hulk #350
Marvel Fanfare #44
Marvel Comics Presents #48 (Storm story)
Iron Man #249-250
Thor #409-410
Spectacular Spider-Man #159
Web of Spider-Man #59
Avengers #311
Amazing Spider-Man #327
Spectauclar Spider-Man #159
Captain America #365-366
Daredevil #275
Wolverine #19
Web of Spider-Man #60
Spectacular Spider-Man #160
Web of Spider-Man #61
Punisher (1987) #28
Avengers #312
Punisher #29
Punisher War Journal #12-13
The Mutant Misadventures of Cloak and Dagger #12-13
Fantastic Four Annual #23 (2nd story)
Impossible Man Summer Vacation Special #1 (6th story)
Alpha Flight #90-91
Excalibur #37-39
Fantastic Four #350
Fantastic Four #352
Avengers #332-333
Iron Man: Legacy of Doom #1-4
Marvel Super-Heroes #8 (3rd story)
Unbeatable Squirrel Girl (vol. 2) #2-5
Infinity Gauntlet #2-6 (and Doctor Strange, Sorcerer Supreme #32-34)
Fantastic Four #358 (2nd story)
Amazing Spider-Man #349-350
Marvel Comics Presents #100
Marvel Graphic Novel: Doctor Strange & Doctor Doom: Triumph & Torment
Fantastic Four #361
Marc Spector: Moon Knight #39-40
Infinity War 1-5 (and Silver Sable #4-5)
Fantastic Four #371-375
Namor: The Sub-Mariner #30-33
Fantastic Four #376-381
Silver Surfer #106-108
Doctor Strange, Sorcerer Supreme #62
Fantastic Four #405-407
Fantastic Four Unplugged #3
Fantastic Four Unlimited #12
Fantastic Four #408-409
Captain America #453
Doom 2099 #40-42
Fantastic Four #413
Doom 2099 #43
Fantastic Four #416
Onslaught: Marvel Universe #1
X-Force #63
Spider-Man Unlimited #16
Fantastic Four #4-6
Iron Man vol 2 #10-11
Fantastic Four #10
Fantastic Four #12
Avengers vol 2 #12
Iron Man 12
Captain America vol 2 #12
Fantastic Four #13
Avengers #13
Iron Man #13
Captain America #13
Heroes Reborn: The Return #3-4
Thor '99
Heroes Return: Doomsday #1
Heroes Return: Masters of Evil #1
Heroes Return: Ashema #1
Heroes Return: Doom #1
Fantastic Four vol. 3 #15-16
Fantastic Four #25
Doom #1-3
Fantastic Four #30-31
Black Panther #27-28
Amazing Spider-Man #36
Thunderbolts #51-52
Doom: The Emperor Returns #1-3
Fantastic Four #50
Fantastic Four #52-54
Iron Man Legacy #1-5
Avengers #59
Marvel Double Shot #2
Amazing Spider-Man #50
Thor #58
Iron Man #64
Avengers #63
Fantastic Four #67-70
Fantastic Four #500
Fantastic Four #507-508
Books of Doom 1-6
Spider-Man Unlimited (2005) #14
Fantastic Four #536-537
Fantastic Four Special (2006)
Wolverine #42
Blade (2006) #2
Black Panther #18-19
Captain America #23
Heroes for Hire #8
Fall of the Hulks: Alpha
Sub-Mariner (2007) #6
Penance: Relentless #4
Thor #5
Mighty Avengers #9-11
Friendly Neighborhood Spider-Man #24
Fantastic Four #557-562
Secret Invasion: Dark Reign #1
Dark Reign: The Cabal #1 (1st and, a bit later, 5th stories)
Dark Avengers #1-4
Dark Avengers vol 2 #176-177
Fantastic Four #562-563
Fantastic Four #566-569
Captain Britain and MI-13 #10
Captain Britain and MI-13 Annual #1
Captain Britain and MI-13 #14
Thor #600-602
Dark Reign: Made Men #1 (2nd story)
Captain America: Reborn #4
Doctor Voodoo: Avenger of the Supernatural #1-5
Thor #603
Thor: Finale #1
Thor #604-606
Black Panther #9-12
Doomwar #1-6
Incredible Hulk #606-607
Hulk #20
Incredible Hulk #608
Hulk #22
Incredible Hulk #609
Siege: The Cabal #1
X-Factor #201-202
Namor: The First Mutant #6-8
Fantastic Four #588
F.F. #1-2
Incredible Hulk #5-6
Avengers: The Children's Crusade #2-8
X-Men #16-19
Incredible Hulk #7-7.1
F.F. #3-5, 8-10
Fantastic Four #600
F.F. #12-14, 16
Fantastic Four #611
Winter Soldier #1-6
F.F. (2nd series) #7-8
New Avengers (2013) #6-7
Uncanny Avengers #21-22
F.F. #10, 12-13, 15-16
She-Hulk #3-4
Fantastic Four (2014) #3
Fantastic Four #5
New Avengers #23
Fantastic Four Annual #1
Loki: Agent of Asgard #6-7
Magneto #11
Avengers/X-Men: Axis #2
Deadpool #36
Avengers/X-Men: Axis #3
Avengers World #15-16
Axis: Revolutions #4 (2nd story)
Avengers/X-Men: Axis #6-9
Fantastic Four #12
New Avengers #24, 26-27, 29, 31, 33
SECRET WARS
Invincible Iron Man (2015) #1-2, 4-6, 9, 12-13
Infamous Iron Man #1-12
Marvel 2-In-One #1-6
Marvel 2-In-One Annual #1
Invincible Iron Man #593-600