I see alot of votes for Magneto. Let's face it thou, he hasn't been a proper villain since the early 90's (and he's been flip flopping between hero and villain since the mid 80's). So while he's a major seminal character in the MU, I don't think that today he can be considered one of their big 3 villains, though I'd put him on the list of biggest three Marvel villains of all time. Sooo, I'll make two lists.
Current Top 3 Villains:
Victor Von Doom
Loki (He's Thors arch, he brought the Avengers together in the comics, and his profile is high because of the recent films)
Thanos (he's been central in more major events than probably anyone else over the last 20 years and has a high profile outside of comics since the Avengers film)
Top 3 Villains of All Time:
Victor Von Doom
Eric Lensherr
Norman Osborn (Might seem like an odd pick but Spider-Man is Marvel's flagship character. Norman Osborn is his arch enemy and that makes him (nearly) just as important. The character is pretty much the Joker and Luthor rolled into one. Plus, like all major villains should, he recently go his chops at trolling the whole of Marvel during the Dark Reign crossover event)
I don't think Marvel has a universal "Big 3" anything. I think each subset of heroes has there own 3. X-Men have Magneto, Apocalypse, Sinister. Avengers have Kang, Ultron, Kree. Spidey has Green Goblin, Dr. Octopus, Venom, etc, etc.
Those are the recurrent ones, after that you have all those appearances of strange entities and overpowered cosmic whatevers. I picked those three because of their long history of being a global threat and because their personalities are really well detailed with a very solid background and each time repercussions on the entire MU.
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