These are all of Doctor Doom’s appearances in the 2000s. Doom is particularly active in this decade, mostly thanks to multiple crossovers where he’s one of the players.
Heroes Reborn: Doomsday
Intermission – Valeria Von Doom (Fantastic Four vol.3 #14 to #24, published 1999 but set during the previous review)
Fantastic Four v3 #25
Intermission – Fantastic Four v3 #26-29
Doom #1-3
Fantastic Four v3 #30-31
Thunderbolts #51-52
Doom: The Emperor Returns #1-3
Fantastic Four v3 #53-54
Marvel Double Shot #2
Amazing Spider-Man v2 #50
Standoff (Thor v2 #58, Iron Man v3 #64, Avengers v3 #63)
Fantastic Four v3 #67
Fantastic Four v3 #68-70
Fantastic Four #500
Fantastic Four #501-503
Fantastic Four #504-506
Fantastic Four #507-508
Doom intermission: Secret War
Fantastic Four #536-537
Fantastic Four Special
Doom 2000s cameos
Black Panther v4 #19
Penance: Relentless #4
Fantastic Four #551-553
Mighty Avengers #9
Mighty Avengers #10
Mighty Avengers #11
Fantastic Four #557-563
Secret Invasion: Dark Reign #1
Dark Reign: The Cabal
Dark Avengers #1-4
Fantastic Four #566-567
Fantastic Four #568-569
Dark Avengers #176-177 (continuity insert from 2012)
Iron Man: Legacy of Doom
Thor #600-604
Thor #605-606
Doctor Doom’s Dark Reign cameos
Black Panther vol5 #1-12
Doctor Voodoo: Avenger of the Supernatural #1-5
X-Factor #200-202
Fantastic Four 1234 #1-4
Spider-Man and the Fantastic Four #3