These are all of Doctor Doom’s appearances in the 1990s. While far from his best decade (at least in main continuity, since Doom 2099 is not part of the retrospective), there are a few gems here and there.
ACTS OF VENGEANCE is covered in the 80s since it crosses the two decades.
There’s also that time Doctor Doom became Santa Claus.
Cloak & Dagger #12-13
Alpha Flight #91
Avengers #332-333
Excalibur #37/39
Fantastic Four #350/352
Fantastic Four #358
Marvel Fanfare #44
Infinity Gauntlet
Triumph And Torment (published in 1989, takes place in the 90s)
Amazing Spider-Man #350
Marvel Super-Heroes #8
Fantastic Four #361
Marvel Comics Presents #100
Moon Knight #39-40
Infinity War #1-5
Silver Sable and the Wild Pack #4-5
Namor the Sub-Mariner #30-33
Fantastic Four #373-374
Fantastic Four #375
Fantastic Four #376-380
Fantastic Four #381
INTERMISSION (during Doom’s exile)
Doom’s 90s cameos
Deathlok #2-5
90s intermission, Part 1 (Doctor Strange, Fantastic Four)
90s intermission, Part 2 (Code Blue, Nova, Fantastic Four)
90s intermission, Part 3 (Fantastic Four)
Silver Surfer #106-108
POST-EXILE
Fantastic Four #404-409
Captain America #453
Doom vs Doom 2099
Doom’s Onslaught
90s intermission, Part 4 (X-Force, Spider-Man, Thunderbolts)
HEROES REBORN
Part 1
Part 2
Part 3
90s intermission, Part 5 (X-Man, Cable, Gambit)
Thor Annual 1999