During DC's One Year Later event, several minor Batman villains were killed off, one of them a mutated biologist named Orca. During the storyline, it's revealed that Orca was married to a normal human, who's interviewed by the police regarding the circumstances around her death. While a little humor is taken from the relationship (the man remarking that he had a thing for big women◊) the pain of loss is treated seriously.
Mr. Freeze loves his wife Nora more than anything in the world, and every single crime he commits - no matter how atrocious - is done with the end goal of curing her illness and saving her life. (It should be noted that the nobility of his intentions varies Depending on the Writer, especially during his New 52 incarnation.)
Likewise, Talia al Ghul truly cares for her son, Damian, in spite of his allegiance to the Bat-Family (though, again, this largely depends on the continuity).
Robin (1993): The General cares for his brother and sister even if he doesn't really get along with them. When he accidentally kills them he blames Robin for their deaths and becomes considerably more dangerous, almost dipping all of Gotham back into a violent gang war and killing anyone who matches his profile for Robin's secret identity.
In Convergence: Green Lantern - Parallax #2, Hal/Parallax is very pissed when Electropolis' princess and her army attack Kyle.
Deadshot, the world's greatest marksman, an unrepentant assassin, sends the money from his hits to his daughter. Secret Six basically has a team of villains forming their own kind-of family.
For all his flaws and failings, Slade Wilson aka Deathstroke does genuinely love his children and his butler Billy Wintergreen. Especially in the DC Rebirth series. However, he is a terrible father; Wintergreen notes that Slade is incapable of expressing his affection for his surviving children in anything approaching a healthy way, and he has no compunctions about lying, manipulating, or endangering them, either.
The Rogues are a close-knit group of criminals who act as a family, albeit a dysfunctional one. They originally got together just out of practicality, and a few of the guys couldn't stand the others. But over time, they realized that they're all the family any of them has. This trope is actually the reason Captain Cold, who had been retired at that point, reformed the Rogues after they disbanded; his only family, his sister Lisa, had just been killed. While he ends up expanding the Rogues to include the newer groups also calling themselves the Rogues, he still only considered the core group (himself, Heatwave, Weather Wizard, and the legacy versions of the Trickster, Mirror Master and Captain Boomerang) as the real Rogues and his family. Among all the Rogues, they will repeatedly state that their group is just a working group and they have no attachment to each other, but they have repeatedly shown that is not the case.
The second Reverse-Flash, Hunter Zolomon, is noticeable for this. While he believe that heroes who've suffered tragedy will come out stronger, and that loved ones are a distraction, he himself still sees the third Flash (Wally West) as a friend, despite the fact that Hunter caused Wally's wife to miscarry. Speaking of which, the quickest way to incur Hunter's wrath is to threaten his ex-wife as the Rogues learned.
New Gods: Despite being utterly evil, Darkseid did truly love his first wife Suli, which is why his mother had Desaad poison her-to ensure she couldn't soften her son. It worked alright, as Darkseid had Desaad poison her. This love he had for Suli is the main reason why he always brings his son Kalibak back despite his contempt for his incompetence.
Pre-Crisis Lex Luthor is as big a bastard as they come, but he loves his family deeply. In the Supergirl strips he goes to extraordinary lengths to prevent his sister Lena and her son from discovering their blood relationship. Supergirl herself states he only looks like a decent human being around his family. In Adventure Comics Vol. 1 issue #388:
Supergirl: But it was a white lie! Luthor doesn't want Val to live with the stigma of having a master criminal for an uncle! This was his one decent act in a lifetime of crime!
In The Girl with the X-Ray Mind, Luthor asks Supergirl why he should help her out. Kara's "Because Lena is being threatened by the Phantom Zoners' scheme" reply gets him to join forces with her.
"The Strange Revenge of Lena Luthor": The whole "a criminal gang gets hired to gaslight Lena" mess starts because of one of Lex Luthor's few good qualities, that he genuinely cares about his sister. In the end, he's even willing to cooperate — a little — with Supergirl to help her.
Syrene is a despicable, power-hungry sorceress, but she really loved her father Ambra. After gaining quasi-omnipotence in Two for the Death of One, her first action is to attempt to kill his murderer.
Superboy Prime: Despite the atrocities Superboy-Prime commits, he still very much loves his parents Jerry and Naomi Kent and his girlfriend and childhood friend Laurie Lemmon. In fact, he becomes a villain because he wants them back after they were erased from existence.
The obsessiveness of Legion of Super-Heroes' villain Lightning Lord's towards his sister Light Lass has creepy undertones; regardless, he goes ballistic in The Earthwar Saga when one minion sensibly suggests him to get rid of his little sister before she becomes a problem.
In her original appearances, Tara "Terra" Markov was eventually revealed to be a cruel, cold-hearted girl with no redeeming qualities. Despite this, she seems to have a genuine sweet spot for her older brother Brion.
Terra: Richard Faulkner and Veronica are both incredibly amoral self absorbed people, but they really do care for each other and Veronica being killed by her exposure to Quixium sends Richard spiraling into madness.
In Tomahawk, Lady Shilling, the sister of Tomahawk's Archenemy Lord Shilling, adopts the identity of the Hood to seek revenge on Tomahawk after he causes her brother's death.
In Trinity (2008), Enigma (the antimatter universe Riddler) is a smug, manipulative bastard who sets in motion a plan to steal cosmic power that throws the whole universe off balance so that he can save his daughter's life.
During the Uncle Sam and the Freedom Fighters miniseries, Lester Colt grew disillusioned with working under the Administration after being sent to kill an Intergang drug runner at his five-year-old grandson's birthday party.
The Warlord: The assassin Y'Smalla is driven by a fanatical level of hatred for Travis Morgan because Morgan killed the man that she loved during is war against the New Atlanteans.
Ares loves his children, even if they're not always on the same page as him and don't always appreciate the things he does to look out for them. Harmonia has outright worked against him at points but even during this period he gladly gave her a protected place to live. The exception seems to be Hippolyta and her sisters, and not all writers stick to the canon of Ares being their father.
Wonder Woman (1987): Circe, who hates humanity as a whole, loves her daughter Lyta, so when Lyta ends up in the care of the Amazons and beyond Circe's reach her hatred of the Amazons is greatly multiplied.
◊) the pain of loss is treated seriously.
