Originally Posted by
DrNewGod
This is a particularly difficult question, because it's very point-of-view based; not only for each reader, but for each in-universe observer.
If you're an average citizen, it's the ones that get on TV: Dr. Doom, Magneto, and maybe...Kang or Ultron.
If you're a knowledgeable mystic, it's maybe the ones you know want to collapse reality: Dormammu, Nightmare, or perhaps Malekith.
If you work at SHIELD, you probably can't pick just three, but the ones that mean the end of the world or civilization-as-we-know-it demand a special share of your attention. The list probably includes at least one among Galactus, MODOK, Loki The Red Skull, or Thanos.
If you work for the Hulkbusters, it's probably The Hulk, followed distantly by The Leader, and maybe The Abomination.
If you work in insurance, you'd probably have special curse words for The Hulk, The Sub-Mariner, and Magneto.
For me personally, Dr. Doom is (and always will be) at the top. If I have to pick two to share the spot with him, I'd say Thanos, and probably Ultron.
Only for about 1/2 Magneto's existence; read anything prior to Uncanny X-Men#1.250, and it's a very different story. I get it, the Magneto that some have encountered has always been an anti-hero (although some refute the very existence of the concept), but he was created as a straight-up mustache-twirler. Don't let Stan's revisionist "memories" fool you, the first ~20 years of printed stories make it clear.