1. Victor von "Uncle" Doom
Let's begin by saying we'll hear no arguments that Doctor Doom is actually, really, truly a good guy underneath it all. Here's a guy who shot a guy for not clapping long enough; who led the first bloody, successful invasion of Wakanda in centuries; and who skinned his childhood crush alive. The dude is bad news, no matter how many times he's saved reality.
That's just it, though. The guy has saved not just the lives of his greatest enemies, the Fantastic Four, time and time again, but all of reality itself. You can see versions of these events play out throughout the character's history.
One notable time comes at the start of Jonathon Hickman's landmark Fantastic Four run. Near its start, Vic and his true rival -- Reed Richards -- learn there's a cabal of multi-universal Reeds out there. Besides acting as "benevolent dictators" (similar to Doom's own role in Latveria, you might say), this Council of Reeds have taken it upon themselves to lobotomize every Doc Doom in their respective realities.
Doom is not pleased. Yet when the best laid plans of Reeds and... other Reeds nearly leads to an invasion of Mad Celestials (Jack Kirby's lovable, unknowable cosmic monsters) Doom stands up. Now normally, when Victor helps save the world it's because he wants it all for himself somewhere down the road. In this instance, however, the last stand is downright suicidal. In fact, while Doom does survive, even he's not sure how, or why.
But we can guess why he might have made this desperate, last stand in the first place. Odds are it's because one Valeria Richards -- daughter of Mister Fantastic and the Invisible Woman -- was in the Celestials' line of fire. While Doom has always had a soft spot for Mrs. Richards, his history with Val has a lot more meaning to it. Victor named and delivered the child himself, and was actually her father in an alternate universe.
Despite Doom's attempt to enslave Valeria, and flaying her namesake (oh, yeah, remember that?) the pint-sized super-genius still sees Doctor Doom as family.
She even refers to him as "Uncle Doom," and treats Latveria as her home-away-from-home when things get rough between Val and her parents. That mutual, familial bond goes a long way to humanize Victor. Even if he's a long, long way from being a hero.
2. Doctor Octopus, The Lethal Lover
Doctor Octopus is one of the clownier Spider-Man villains. He's a big nerd with a bowl cut, triangle shades, and who's claim to fame is having four more limbs than most of Peter Parker's nemeses.
At least that used to be the case. Over the years, Otto Octavius has become more textured -- not to mention threatening. Despite his nerd-ly origins, Doc Ock was alpha enough to bring together the original Sinister Six, bro. Later, ups his own ante considerably by trying to cook half the planet with juiced up sunbeams, while letting the remainder remember him with awe and fear as a sort of vengeful god. We... should mention that he was dying at this point, which might account for the upgrade from "thorn in Spider-Man's side" to "oil industry levels of solar genocide."
Throughout it all, though, Ock showed that he had a softer side. At the very least, he has human needs and desires. That most basic of which is, of course, the need for human affection. Yeah: ridiculous haircut or not, Doctor Octopus is actually one of the more lovey-dovey villains in the Marvel rogues gallery.
The first hints of this are made relatively early in the grand scheme of comic books. In one now-classic story, Otto opts to marry May Parker, known to some by her street name, "Aunt May." While this was actually a ploy to steal an island May recently inherited, signs since have shown that Doc Ock actually harbored feelings for the woman who raised Peter Parker. They even had sex, as Pete horrifically witnessed when searching through his enemy's memories.
After the botched wedding, but before Spider-Man's accidental peep show, Doctor Octopus teamed up with fellow supervillain Stunner. Besides a business relationship, the two were lovers. Later, when Ock-y seemed to have succumbed to his terminal dying-ness, Stunner event sought revenge against Spider-Man for killing her "beloved"
Of course, this just so happened to take place during the brief period in which Otto had taken over Spider-Man's body and identity in the much-better-than-it-had-any-right-to-be series, Superior Spider-Man. Like many great comics, it sounds completely idiotic until you read it.
Speaking of Superior Spider-Man, it was during this run that Doc Ock/Spider-Man fell in love with Anna Maria Marconi. Doc Ock isn't known for respecting other people's intellect, but Marconi's brain got him off his high horse long enough to fall in love again. So much so, that it was Anna Maria who inspired the parasitic memories of Otto Octavius to let go, and give Peter Parker his body back.
While three, whole relationships in a lifetime might sound pretty average, it's well above that for comic book villains -- whose romantic entanglements usually begin and end with poorly conceived sexual assault stories... Doctor Octopus might not be the Earth-616's greatest lover, but his interpersonal attachments make him just a little bit more believable than many of its characters.