Cool shit. I'll try and do some extra ones. See if you agree/disagree.
Batman: Ra's Al Ghoul. Don't know how you can pick another, really.
Superman: I'll go with Braniac right now. When the New Krypton endgame comes, I'll probably say Zod.
Spider-Man: Kraven. Yes, he died a long time ago. But when I think of villains who make me think "Wow, Spidey is fucked," it's Osborn, then Kraven.
Flash: Captain Cold. I love this character. The other Rogues waver between evil and pathetic, but Snart is just fucking scary bad. Grodd is a close second for me.
Green Lantern Hal Jordan: Black Hand. I think it's pretty much a no-brainer by this point of Blackest Night.
Captain America: Baron Zemo. The airplane blowing up is a seminal moment of the character's history, as was the formation of the Masters of Evil
The Fantastic Four: Galactus or Namor. It's hard to even think of someone other than Doom for them, huh? Truthfully, though, it seems like every mad scientist villain in the Marvel U thinks of Reed Richards as his greatest rival, so it's really hard to pick.
The X-Men: Apocalypse, I guess. But, really, they have villains coming out of the woodwork, so it's a pick-and-choose.