If I have children and subsequently grandchildren, I will keep my three-year-old granddaughter near me at all times. When the hero enters to kill me, I will ask him to first explain to her why it is necessary to kill her beloved grandpa...
Played straight and averted in Death Note where Light does indeed care for his family, even after his descent in morality. When his sister was kidnapped by Mello, he couldn't bring himself to kill her with the Death Note and the result was Mello acquiring a Death Note of his own as ransom.
Fun fact: It was hinted at in the Sevii Islands quest in Fire Red/Leaf Green. This is foreshadowing for PokéSupe, as it did come out before the FR/LG section of the manga, but who knows how long the manga writers had been planning that.
They may have been sociopathic assholes, but the three Trinity siblings of Gundam 00 did really love and protect each other. And Nena genuinely cried and mourned when Michael and Johann got killed..
Fuhrer King Bradley is one of the homunculi, but he shows affection for his wife.
Another homunculus, Pride, also shows affection for one person: his "mother", Mrs. Bradley. This is surprising, as Pride is by far the most evil of all the homunculi.
There are also two chimera henchmen who turn to the path of righteousness when they find out their families will likely become victims of the Evil Plan.
Also implied with Van Hohenheim, but it's a Red Herring. He's not evil at all, but for a while viewers are given the false implication that he and Father (who doesn't have loved ones at all) are the same person.
Flame of Recca does this. Despite being a sadistic bastard of an assassin, it's made pretty clear Kurei has underlings who care for him. He clearly returns their loyalty, although in his own way, mourning them if they die and swearing revenge on their killers. Neon even falls in love with him, and they become a couple. As it turns out, he intends to take revenge on Kouran Mori because Mori murdered Kurei's first love.
Calling Jeagar, one of Rex Godwin's most important henchmen from Yu-Gi-Oh! 5Ds, evil might be a stretch (selfish and arrogant, maybe, but probably not evil). Still, he does have a wife and son that he cares deeply for and tries his hardest to protect, so he still fits this trope.
Johan Liebert in Monster has loved ones, too, but it makes him more, not less, disturbing. Because to find and reunite with his estranged twin sister Anna, he actually kills her adoptive parents. This one is an "iffy" case, because it's hard to tell if Johan actually loves her, or if she's simply his favorite experiment, as he may be incapable of love at this point.
Gin Ichimaru from Bleach appears to be evil to the core, but at least somewhere amidst the many, many things he did For the Evulz was a long and subtle plot to kill his boss Aizen for hurting his only friend, Rangiku, when they were both kids.
Several of the Arrancar also demonstrate this tendency, most pointedly Tia Harribel and Coyote Starrk, who are both very attached to their Fraccion. When Tia thinks hers have been killed, she becomes furious and would have killed Toshiro if he hadn't been quick enough to set up a decoy maneuver he'd been saving for Aizen, while Starrk in the anime seems to lose his will to keep fighting when Lilinette dies protecting him, and is soon slain by Kyoraku. Even Loly and Menoly, two arrancar girls who are noted mostly for their psychotic grudge against Orihime, appear to have genuinely loved each other, as Menoly supported Loly despite her massive and justified doubts about attacking Orihime a second time and Loly went berserk when Menoly was killed.
The Fraccions also share such feelings, as Lilinette's last words are her calling out to Starrk in anguish, and the novels show that the three girls from Tia's group would rather ask a human like Orihime for help than let their leader die. One of them even refuses to have her own considerable injuries healed first (and the three had barely survived being torched alive on top of mutilating themselves to create a Chimera), so anxious for Tia's recovery she was.
Played straight and subverted in the Vandereich arc. Royd Lloyd plays it straight, as while he was disguised as his leader Yhwach, he reacted with genuine grief and horror when Yamamoto summoned a Quincy Army of the Dead (which suprised Yamamoto himself). Subverted when the real Yhwach appeared: as the mortally injured Royd smiled as he bled to death, he briefly congratulated the guy for his work... and then gave him a "You Have Outlived Your Usefulness".
Suboshi from Fushigi Yuugi had a twin older brother named Amiboshi, and when he had jumped off the slippery slope after thinking the kid was dead (as in, he killed Tamahome's family as revenge for supposedly killing Amiboshi, he still cared for his twin. Tomo learnt it the hard way, indeed.
Also, Nakago and Soi, though it doesn't seem so at first. After Soi is killed, Nakago is obviously very pained to lose her, and keeps her body with him
The Noah from D.Gray-Man genuinely care for each other. When one of them was killed (Skinn), they held a funeral for him and cried for his death.
It's not just emotional connections. They're perfectly willing to kill everyone in the vicinity just to avenge one of their members. The place they come from, the Falling Star continent, is even worse. The bonds they hold for their fellow brethren are so strong, they were willing to kill themselves to blow up 31 people who were responsible for 1 of their own simply being falsely imprisoned. What makes it so chilling is that despite being the "bad" guys, they possibly treasure each other just as much or even more than the heroes do their own friends.
Backfires again when Neferpitou begs Gon to let him heal Komugi, the Chimera Ant King's Morality Pet, after she is injured during the Hunters' attack. Gon is furious, refusing to believe that the same person who made Kaito into a puppet who Gon doesn't know is already dead is begging for the life of another.
Dark Oak of Sonic Xdeep down inside, is actually not all that bad. That's because he actually cares for Hertia/Earthia, and was worried that he might never see her again after she abandoned him on his former homeplanet with many other dying males and only a few surviving ones.
Kurojaki from Ginga Nagareboshi Gin. He's one of the strongest and most ruthless villains in the manga, but he cares deeply about his son. When he thinks the little pup has been killed, he's devastated and goes into a beserk rage as he takes on the entire pack of dogs at once.
Hougen from the Sequel SeriesGinga Densetsu Weed may be a murderous Jerkass, but the only dog he cares about is his brother Genba. It turns into a Tearjerker later on when it's revealed that they made a promise to each other. And that was if one brother was to die, his brother would be the one to kill him. So Hougen did the only honorable thing we see him do: fulfill that promise.
Before The Reveal, Naruto fans considered Itachi completely evil and heartless. Then we found out how much he cared about his little brother. He was supposed to wipe out the entire clan, Sasuke included, but he couldn't do it. There's no denying that Itachi worked for the bad side and did horrible things but he had Big Brother Instinct. This example is harder to see then most cases because he Mind Rapes Sasuke on two occasions.
There was also his loyalty to Konoha. Everything Itachi's every done was ultimately to protect his home, and his Undying Loyalty to his village has not faded at all, regardless of how much time has passed and how much they made him suffer. In fact, Sasuke's the only one Itachi's ever loved more than Konoha. It was Itachi's devotion to the village that ultimately fuels Sasuke's decision to side with Naruto against Madara.
Obito Uchiha genuinely loved his teammate Rin; when she died at Kakashi's hand it broke him and lead him to accept Madara's plan, beginning his Start of Darkness. Ultimately, he enacted Madara's Eye of the Moon scheme because he wanted to live in an illusion where he and Rin were living happily together just as much as he wanted to put everyone else into a mind-controlled paradise.
Later chapters reveal that Obito's entire world ultimately revolves around his team, not just Rin. His ideal world is a reality where not only was Rin alive but one where Kakashi and Minato were together with them, living up to the ideals that drove Obito during his youth.
In Mai-HiME, Alyssa and Miyu are willing to destroy the school to advance the Searrs' plan, but they deeply care for one another (albeit in Alyssa's case, not quite as much as for her father), even though they are not considered as human by the rest of Searrs (Alyssa for being an artificially created Hime and Miyu for being a robot). Similarly, Nao, one of the more antagonisic Hime who did not become so out of love, considers her mother her most important person and is devastated when Shizuru destroys her Child, killing her.
In Muhyo And Roji, the Cortlaw siblings vary in alignment (Mick is definitely evil while Kid is more innocent and a victim of manipulation), but they all care for each other, and seek to bring their parents back to life.
Rurouni Kenshin: Shishio Makoto, despite being the Darwinian, totalitarian, Big Bad of the Kyoto arc, and for being the subsequent cause of her death, truly loved his consort Yumi and was the only person who really valued her as a human being. In fact, Shishio became very offended when Kenshin implied that he didn't love Yumi for taking advantage of her position by stabbing her in order to stab Kenshin. As it turns out, it was what Yumi wanted all along, and Shishio honored such an action via holding her in his arms as she died. They're eventually reunited in the afterlife, which for them, is hell.
In Roanapur, Revy Two-Hands is one of the most murderous people around...but she comes to care about Rock. Hit Rock, hurt Rock, kidnap Rock...and Revy will come for you. If you're lucky, she'll kill you quickly. Otherwise...
She's not the only one. Balalaika cares about each of her Vysotniki. Kill a Hotel Moscow man, and Balalaika will take it very personally.
Doflamingo in One Piece is shown to have a soft spot for his most loyal, reliable crewmates. When Monet prepares to blow up Punk Hazard, he is visibly saddened and later when Monet didn't respond (having her heart incidentally squeezed by Caesar), he directly goes to the place himself to find out the reason why. At one point, he even apologizes to Vergo, calling the latter a companion and in other words a friend. An Alternate Character Interpretation of him, by another henchman's account, killing all of Baby 5's fiances was because he was concerned for her, seeing how she tended to accept proposals from swindlers and sleazes, his actions might be seen as an extreme Big Brother Instinct. Later chapters reveal that his relationship with that of his highest executives are akin to those of a family; they have shared both joy and sorrow with him, so he will not tolerate any disrespect towards them.
In Kamisama Kiss Kirihito doesn't hesitate to smash a magical artifact which is spewing poison when he hears his mother's voice.
In the world of Baccano!, being an unrepentant murderous bastard doesn't mean you can't fall in love. As Ladd Russo, who really cares for his fiancée Lua in his own Mad Love way.
Ladd Russo: What, is a mass murderer not allowed to fall in love like a regular person?
Jakotsu is a massive He-Man Woman Hater and Combat Sadomasochist, yeah. However, he is honestly loyal to Bankotsu. In the anime, is shown that they were together even before forming the Band of Seven, and when he gets Suikotsu's Shikon shard he hands it to Bankotsu without hesitation instead of taking it and its powers for himself.
Similarly, Bankotsu is a trigger-happy killer Blood Knight but genuinely cares for his fellow Seven members and does NOT tolerate any harm made to them. He's seen mourning Mukotsu, Kyoukotsu and Ginkotsu after their deaths, and the reason why he was pissed enough to kill Renkotsu in a duel was because he killed Jakotsu.
Ciel Phantomhive of Black Butler is a full-on Villain Protagonist who is primarily motivated by revenge and doesn't mind killing people who get in his way, but he clearly cares very much for his fiancée Elizabeth. Though he'll huff about how it's a waste of time, he'll go out of his way to please her— letting her throw parties in his house, having an Easter egg hunt because she wanted to, and throwing himself in front of a bear for her. He also tries to protect her from the gruesomeness of what he does, even now that he knows she's secretly a Little Miss Badass.
The Titan spies in Attack on Titan are the cause of the world going to hell in a handcart, but god, do they love each other. They freak out when the others are hurt, prioritize protecting each other over the mission, and when they hear that Annie is being tortured, the meek Bertolt reacts by swearing to kill Armin. To some extent, this affection extends to the heroes as well. Due to Becoming the Mask, Annie spares Armin twice when killing him would have prevented her being found out and Reiner is injured and nearly throws himself out a window to protect Connie. It isn't until things hit rock bottom and Bertolt is injured that Reiner actively begins trying to harm his former comrades. That Evil Has Loved Ones turns out to be a major advantage to those among the heroes willing to exploit it.
This appears to hold true throughout the various arcs of Kenichi: The Mightiest Disciple. Some Ragnarok members were True Companions such as Thor and Siegfried. YOMI has Rachael and Ethan who are loyal siblings. This is however ironically most apparent in YAMI. There are various masters sharing an almost paternal bond with their disciples such as Alexandar and Boris or Agaard and Koukin. Some of them are even an out and out Parental Substitute like Akira and Shou or Mikumo and Chikage. The last part cuts both ways, some YOMI disciples faithfully search for their missing mentors when their defeated masters are thrown in a secret jail.
Oriko and Kirika, of Puella Magi Oriko Magica, have this as their main motivation. Though Kirika's feelings are obvious from the outset, Oriko initially seems to be only using her for a greater purpose of saving the human race. However, when questioned as to why she killed dozens of innocent people, she looks at Kirika's corpse and says "To protect my world."
In JoJo's Bizarre Adventure, two of the most evil characters have parents that love them dearly. In part 3, J. Geil is a serial rapist and murderer. His mother, Enya Geil, loves him dearly and when he is killed by the brother of one of his victims, she is devastated and declares her intent to avenge him. Later, the Big Bad of part 4, Yoshikage Kira, is a serial killer with a hand fetish who kills women and saves their hands as "girlfriends". His father Yoshihiro Kira loves him so much that after dying, he stuck around as a ghost and will go to any means necessary to get rid of anyone who could threaten his son.
They may be monsters that live by devouring humans, but more than one Awakened Being from Claymore turns out to be capable of genuine love for others. Riful of the West and her consort Dauf are fairly dysfunctional, with her constantly berating him and threatening to leave him. But when both are seriously injured in battle, they refuse to abandon each other. Isley ends up taking an amnesic Priscilla and the human Raki under his wing, and realizes that their years spent together were a happy time for him, referring to them as his family. As he's being devoured by the Abyss Eaters, he thinks of how he would give anything for that time with them to have lasted longer. And the third Abyssal One, Luciela of the South, is overjoyed upon being reunited with her younger sister, Rafaela.
Gokukoku No Brynhildr has a twisted example with the Big Bad, Chisato Ichijiku, who is willing to commit any number of atrocities, up to and including killing the rest of humanity, if it means he can resurrect his dead sister.
Rosario + Vampire: Despite being members of Fairy Tale, Aqua and Kahlua Shuzen deeply love and care for their little sisters, Moka and Kokoa, though this won't necessarily spare said little sisters from their wrath. In fact, when their motherGyokuro ordered her to kill Kokoa, Kahlua literally begged her to reconsider.
The Hood is a textbook example of this trope, using some of the proceeds from his criminal activities to pay for his mother's care while also supporting his pregnant girlfriend Sara.
The main villain the Hood "fights" during his first mini also counts; he loves his family greatly and was trying to find a mutant to be part of his supervillain squad because his daughter was one and asked him to hire some more.
In Frank Miller's To Hell and Back, the corrupt precinct captain Liebowitz lets the local crime lords run their businesses without interference, but when they worry he might be wavering, they threaten his family and break his son's arm. His response is to splatter his contact's brains across an interrogation room.
Liebowitz: You shouldn't have threatened my family. You shouldn't have beat up my boy.
Doctor Doom's adoration of his deceased mother, Cynthia, is possibly his only unambiguously good trait. Not only that, but he simply adores Valeria Richards, and swore on the moment of her birth (which he aided in), that he would defend her with his life, and that any one who sought to do her harm would have to deal with his wrath.
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.
Marvel villains Absorbing Man and Titania are both mean, violent thugs, but are married and genuinely love one another.
Averted in terms of Absorbing Man's ex, who is Stonewall's mother. Stonewall is the result of Creel raping Jerry's mother, and Creel doesn't care about Stonewall either.
Used very well with the Kingpin who appears in Ultimate Spider-Man, as Daredevil decides that the only thing a man like him would understand is the murder of his wife, and Spider-Man has to try and convince him that enacting this plan would make them as bad as each other. All this happens while the Kingpin and his henchmen are in the room, by the way.
From what we've seen in flashbacks, he loved Betty's mother Karen too; her death from cancer left him emotionally devastated.
The Sandman apparently had a mother he loved too much to let her know he lived a life of crime, so he changed his name to Flint Marko. When he was bitten and seemingly killed by Venom, he asked Spider-Man to tell his mother he was sorry for not being a good-guy.
In the Spider-Man comic "The Coming of Chaos", Spider-Man discovers that Loki has a mortal daughter named Tess Black (among hundreds of others). Tess gets possessed by a powerful agent known as Morwen - who is a threat to Loki's power. If he didn't care about Tess, he would have killed her in order to stop Morwen. But apparently, he does not neglect his children, and at first demands Tess's release. When that fails, he asks for Spider-Man's help to save her, they go through a difficult process in order to get Tess back alive which causes more problems, and at the end of it Loki admits that he owes Spider-Man a debt for helping him save her. Yep, the God of Mischief and resident Magnificent Bastard is a Papa Wolf. Who knew?
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.
Kang the Conqueror and his love for Princess Ravonna. He even sought out The Fantastic Four, his arch nemeses, in order to save her from a traitor.
A collection of GI JOE comics detailing backstories of characters shows that part of Major Bludd's motivation to continue working for COBRA is the affluent lifestyle he is able to provide his family by doing so.
Norman Osborn genuinely loved his deceased wife. Whether he loves his son or not depends on the writer.
Spider-Man villain and mobster Tombstone is pretty ruthless in the business but, as shown in The Superior Foes of Spider-Man, he still deeply loves and cares about his daughter. In a rare instance of the loved ones also being villainous, said daughter is Janice Lincoln, the supervillain known as Beetle; she also is shown to love her father. In another twist on this trope, Janice was well-aware of her father's lifestyle and business (in fact it was partly what inspired her to become a supervillain, much to Tombstone's consternation) but still had a fairly normal childhood.
Daredevil and Spider-Man foe Kingpin is a ruthless Manipulative Bastard mob boss who rules the New York underworld with an iron fist. However he deeply loves his wife and son, even after both tried to murder him. They both died which has done nothing but make him more cold and bitter. He later fell in love with a woman named Marta and tried to leave the business to be with her. When Lady Bullseye and the Hand killed Marta, Fisk came back to New York with a vengeance.
Another Daredevil foe Bullet, a professional assassin, has an autistic son Lance. Lance is the one thing in the world Bullet cares for and he'll do anything to protect him.
In the Jackie Chan Adventures fic Queen Of All Oni, Jade honestly cares about her dog Scruffy, and breaks the Dog Talisman to make him immortal again, and pampers him a lot for a while, and after Scruffy decides to leave her because of how evil has consumed her, she has a Villainous BSOD.
O'Malley from the Red vs. Blue AU Murderer's Row shows a twisted, rapey, interest in Doc. On a more platonic note, he and Gary are, in flashback chapters, shown to be quite friendly with each other, and O'Malley was extremely upset when Delta killed Gary for a perceived betrayal.
Discord also begs the Dark World!Mane Six not to hurt Screwball and Mad Tiara/Diamond Tiara, who are his nieces. He even sends the two of them away with specific orders to never try to fight the mane six for his death because they'd not stand a chance and likely die.
Despite all the evil, horrible things they've done, Nightmare Paradox and her Psycho Rangers seem to genuinely love each other as friends, to the point they can still use the Elements of Harmony. Paradox has even been looking for a Nightmare Rarity because of what it'd mean to Banneret. Nightmare Banneret and Mirror also still care for Rarity and Apple Pie as well, but not enough to spare them (though its implied Mirror may have spared her Apple Pie in some way).
In the Ponies Of Olympus series, Chrysalis seems to honestly love her daughter Aurelia.
One of the later chapters of A Marauder's Plan featured Barty Crouch Jr. reminiscing about his love affair with Rabastan Lestrange and Bellatrix's offer to carry a child for the two of them.
In Marie D Suesse And The Mystery New Pirate Age, it is unclear how much Madelyn, really cared for her lover, Trafalgar Law, and she caused her brother, Monkey D. Luffy's execution for his sake. However, she greatly cares for her husband Garreth, and her daughter Marie, to the point at which she begs Law to exact his revenge on her, rather than him. He replies that he didn't wait 20 years to settle for that, and there is a way for her to right her wrongs- but it involves changing the past so that, among other things, she never meets them.
The Grinning Snake, was written by someone who was upset about Shizuru being a Karma Houdini in Mai-HiME, noting that all the people she killed at the First District had loved ones whom they left behind. In the fic, the daughter of one of her victims makes a contract with Ai Enma and sends her to Hell.
In The Prayer Warriors, Horus has a wife named Baste, and mourns her passing after the Prayer Warriors kill her, and before they cause him to suffer the same fate.
In the Hunger Games fanfiction Some Semblance of Meaning, District One tribute Obsidian reveals in his interview that he volunteered not only because he wanted to compete in the Hunger Games but because his thirteen-year-old cousin was the male tribute who had been selected. (Then again, Obsidian isn't really evil, even if he is part of the Career pack.)
In TheMasksWeWear both Zuko and Azula are horrified by the thought of their father dying as a result of his insisting on using lightning redirection immediately after learning it. He succeeds.
The Rise of the Guardians fic Guardian of Light, Pitch is revealed to be Helen's father. While his treatment of her towards the beginning leaves much to be desired, it gradually becomes apparent that he really does love her, despite everything.
Another Rise of the Guardians fic called Lullabies, by the same author as the above, has another example. Jack is surprised by the knowledge that, out of all of the Immortals, Pitch is the only one who has experience in parenting because he has a daughter.
The Star Trek fic Safe and Sound solidifies what the second film established; that Khan cares about his crew. He even adopts the newly augmented Lucille Harewood and accepts her into his family.
Briefly used in the first Spy Kids movie when Floop informs the Big Bad he has built soldiers for him and to demonstrate their effectiveness asks him to disarm one. Then an evil robot kid looking exactly like his son runs in the room, the Big Bad does nothing and the kid knocks him to the floor.
Floop: You hesitated. Lisp: I had to - he's my son. Floop: Are you sure? [kid's eyes flash]
In The Proposition, Charlie Burns is a criminal, but he loves his little brother Mikey and wants to protect him, almost enough to kill his other brother Arthur at Captain Stanley's order. Arthur is a psychopath but loves both his younger brothers and the rest of the Burns gang intensely, and thinks Charlie quite reasonable in choosing to buy Mikey's freedom with Arthur's life. In the end, they team up to bust Mikey out.
Darth Vader of Star Wars fame has Luke Skywalker. Vader's fatherly love for Luke also the entire reason behind Vader's various [[attempts to turn Luke to The Dark Side: the Emperor originally wanted Luke killed before Vader convinced him otherwise. This ends up being what ultimately causes Vader's Heel-Face Turn in Return of the Jedi.
Bill, Beatrix/The Bride and Vernita from Kill Bill are all merciless murderers as well as loving parents. Also, Budd's sword has the inscription: "To My Brother Budd, The Only Man I Ever Loved. Bill"
The Bride's horrifying dilemma about killing Bill in the end stems from the fact that she finds out he's actually a good daddy to their child, BB. The little girl is well taken care of (though her train of thoughts is... special), knows that her mommy isn't dead, and actually is very happy to meet up with the Bride since Bill had told her that she would come to visit her someday (though he didn't tell her what for...). The scene in which The Bride is given the shock of her life once she sees BB when she's about to sneak in on Bill to kill him is perfectly played as well.
In The Dark Knight, the mob are shown in several scenes sharing camaraderie. One in particular has two gang bosses (The Chechen and Salvatore Maroni) eating dinner together. Subverted by the Joker.
Batman: He must have friends! Maroni: Friends? Have you met this guy?
In The Dark Knight Rises, regardless as to whether it's a platonic relationship or a romantic one, Bane and Talia clearly love one another, enough for Bane to rescue Talia and keep her safe in the Hellhole Prison and help her in her plan, and enough for Talia to stand up to her father when he wouldn't accept Bane.
Pando, the main antagonist of Two Hands, is an Affably Evil gangster and a killer — who has a young son whom he clearly adores, watching kiddie TV with him and praising him for the origami pterodactyl he made. This goes back to the main theme of the film that bad people have some good inside them and good people have some bad inside them, as represented by the yin & yang.
In the Mexican film El Infierno, which deals with the violence of the drug cartels, "Cochiloco", one of the most ruthless drug cartel enforcers takes the protagonist to his home and introduces him to his wife and children. Cochiloco then glosses over this by saying "What? You thought I lived in a cave and ate human meat?". However, later his employer kills his firstborn in retaliation, triggering his Roaring Rampage of Revenge.
Max Shreck in Batman Returns convinces The Penguin to capture him instead of his son Chip.
Karl in Die Hard grieves over McClane killing Karl's brother.
Used again the Die Hard with a Vengeance when Simon reveals that McClane killed his brother, Hans, despite Simon revealing that he hated his brother.
Simon:"There's a difference between not liking one's brother, and not caring when some dumb, Irish flatfoot drops him out a window."
Wah Sing Ku (Jet Li) at the end of Lethal Weapon 4 is attempting to flee Riggs and Murtaugh with his brother, all the other villains having been killed. When Murtaugh shoots Ku's brother while aiming for Ku himself, Ku sticks around and tries to kill Riggs and Murtaugh in revenge. Riggs then shoots Ku underwater after they fall off a pier while fighting.
Vogel (Nazi war criminal) in The Debt is married to a nurse at his office, who is horrified when told that her husband has had a heart attack.
Mallory Knox in Natural Born Killers. She killed or helped kill dozens of complete strangers, but she doesn't lay a finger on her younger brother and stops Mickey from hurting him as well.
In Alfred Hitchcock's Foreign Correspondent, the Nazi spy villain loves his daughter. At one point, the heroes try to use that against him by tricking her into going off on a trip to the country with one of them while the other tells the villain she's been kidnapped and will be killed if he doesn't release the diplomat he has abducted. At the end of the film, the plane carrying the villain, his daughter, and the heroes is shot down over the Atlantic, and the villain allows himself to drown so he won't weigh down the bit of wreckage his daughter is clinging to.
Loki in Thor. Despite everything that happened, his brother, his mother, his father, and his friends still love and care for him. Even though he may not show interest in the lot of them once he realizes he is adopted
Taken had Bryan slaughter endless mooks and the members of a human trafficking ring to rescue his daughter from being turned into a sex slave. Taken 2 reveals the bad guys had family, and they're not happy...
Murad: He slaughtered our men, our brothers, our sons. We will find him. We will have our revenge.
Used in a rather twisted way in The Crow. Top Dollar, as depraved a villain as he already is, seems to genuinely love his sister despite the incestuous nature of their relationship.
In Hobo With a Shotgun, Drake opens the film by executing his brother for no reason other than to intimidate the townsfolk, and spends most of his free time abusing his son Ivan. His other son, Slick, however, is one of the few things in the world he gives a damn about, and he shows genuine affection towards the boy. When the Hobo blows out Slick's groin and leaves him to bleed to death in a phone booth, Drake is utterly crushed, and goes from just playing around to calling in the Plague.
Subverted in Stardust. When two of the three evil witches are killed, the third, main witch acts as though she's grieving for her sisters, and pretends that she's about to let the protagonists go, because immortality seems empty without her sisters... only to reveal that she was just toying with the main characters.
Played straight with the Princes, however. They are fine with killing each other to be King (because that's how their father earned his place on the throne), but Septimus reacts with offense when the King asks him if he killed their missing sister, Una. When the Princes finally reunite with her during the Final Battle, (although they're ghosts) they all joyfully shout, "Sister!"
In Act of Valor, Christo, the leader of the drug smuggling and arms-trafficking cartel, has a wife and daughter and loves them deeply. This fact is what Miller uses to break him when he is interrogated late in the movie. Not through threats. Miller simply tells Christo that he will never see them again and spend the rest of his life in prison if he doesn't cooperate.
Miller: (shows Christo a recording of him and his daughter) I wanted you to see that, so you would think about some things very seriously. 'Cause you're going to be sitting in a box somewhere. You'll be treated properly and humanely. But that girl is going to grow up, and get married, and your wife is going to find someone else, and you're going to miss everything. (....) If I had done something to endanger my family, I would feel just like you do right now.
When Candie is killed by Schultz in Django Unchained, Stephen, his head house slave and father figure, and arguably the most villainous character in the film, bursts out screaming and rushes to his side, cradling his body in his arms.
In Star Trek Into Darkness, Harrison's actions are partially motivated by a desire to find and save his former crew.
Harrison: Is there anything you would not do for your family?
And Admiral Marcus does love his daughter and pauses to have her transported to safety before opening fire again on the rest of the Enterprise, who she was pleading for him to spare.
In the 1966 Batman: The Movie, the Penguin uses a dehydration machine to temporarily turn a group of minions into powder (so as to be rehydrated later to attack Batman). As the powdered remains are collected for transport, the Penguin takes pains to tell his mooks to be careful because "every one of them has a mother" (which actually makes their later implied deaths during a later fight scene a little disturbing).
In Man on Fire, 'The Voice', the mastermind behind the kidnapping scheme, turns out to be a divorced man with a family he deeply cares about. He's shown with some of his children, while Creasy specifically gets him to release Pita by threatening to cut up his family and starts with his brother.
Small Soldiers: The Commando Elite, in spite of being genocidal plastic action figures, are visibly distressed and shed Manly Tears at the death of Nick Nitro.
Tony Montana in Scarface (1983) tries to take care of those he loves even as he becomes an increasingly bigger criminal and general jerk. His affection for Gina in particular is very strong, although laced with incestuous implications. Subverted later in the film, as he eventually becomes a malignant presence in their lives when he drives Elvira away, kills Manny because he proposed to Gina, and locks Gina up in his own mansion out of an obsession with "protecting" her.
In Road House, extortionist businessman Brad Wesley loves his sister enough to promise her to look after her only son by forcing the owner of the Double Deuce to make him the bartender, even if his nephew is a stupid failure.
In the 2004 King Arthur, Saxon King Cerdic is a violent Blood Knight who invades Britain mainly for a campaign of Rape, Pillage, and Burn, but he does seem to care for his son and second-in-command Cynric. He threatens to cut his son's tongue out if he openly defies his authority again, but he seems quite willing to die by his hands if his son were strong enough to overthrow him. Later he refuses to kill Cynric for a defeat against Arthur's forces when Cynric offers his life, and when he sends in the last of Cynric's auxiliaries into an obvious death trap during the final battle he keeps him by his side to keep him from harm.
Face/Off: Castor Troy genuinely loves his eccentric idiot-savant brother Pollux. He refuses to kill him even after Pollux accidentally betrays their location to Archer by personally paying for the private jet (instead of letting one of their cronies do it) as most terrorists would have, sheds tears when Pollux dies and even ties his shoelaces for one last time before leaving.
Erik grows to love Charles as a brother over the course of X-Men: First Class, but that doesn't stop him from betraying his best friend or abandoning him.
In The Wolverine, Ichirō still seems to care for Mariko to some degree, given he purposefully diverges his sword slash not to hit her when she gets in the way.
Byron De La Beckwith (James Woods) in Ghosts of Mississippi, an unrepentant racist and murderer, gets a quick scene playing patty cake with his granddaughter while the jury deliberates.
Sawney Rath in the Redwall book Taggerung did seem to start out genuinely liking his adopted/stolen son Tagg. Then Tagg went and messed everything up by being of a good species, and Sawney tried to have him killed, and things went downhill just a tad. Ferahgo, in Salamandastron, openly announces that if he finds out his son Klitch is in on the plots against his life, Klitch will be allowed to live "because he's my son".
In the Harry Potter series, the entire Malfoy family has no morally positive traits, save for that they genuinely love each other, culminating when Narcissa Malfoy lies to Voldemort to save her son and gets away with it. In fact, since that lie ultimately resulted in Voldemort's death, the Malfoy family was pardoned for their crimes.
Narcissa's sister, Bellatrix, who is the worst of the Death Eaters, also seems to have a close relationship with her; she calls her Cissy, and she's confident that Narcissa wouldn't hurt her, because they're sisters.
In Snape's case, his love for Lily is strong enough to provoke a Heel-Face Turnbefore the books even start.
In the Sherlock Holmes novel The Hound Of The Baskervilles, the escaped Serial Killer Seldon is still loved by his older sister Elisa. Upon seeing Elisa's completely heartbroken reaction after Seldon is accidentally killed by the Hound (Seldon was wearing old clothing belonging to the Hound's intended victim, and smelled like him as a result), Watson comments "Evil indeed is the man who has not one woman to mourn him." Which, although Watson doesn't make the connection explicit, tells us something about the villain of the novel, whose death at the end is mourned by nobody; the one woman who might have been expected to mourn him seems positively glad he's gone.
Very common in A Song of Ice and Fire; many villains are saved from being truly despicable by their love for their families. In fact it's quicker to list the subversions/aversions/inversions:
The Late Lord Frey is a bastard to everyone, but anyone who dares to mess with his children or grandchildren had best be prepared to suffer... and it's this reflex which caused him to cross the Moral Event Horizon. Robb Stark insulting his daughter led to the Freys switching sides and a massacre of the Stark forces known as the Red Wedding. Yet this turns out to come right back around at him because revenge for the Red Wedding ends up killing more of Frey's family then the war ever did. It's also possible that this is more about preoccupation with family honor than any real affection because when Catelyn tries to take his grandson Aegon the jester hostage in exchange for Robb," a son for a son", Lord Frey lets Aegon die because he's not of any particular use.
Subverted with Roose Bolton and his bastard son Ramsay; they're close because they're both verynasty men, although even they have at least some attachment to certain people. Roose cared enough about his trueborn son to warn him not to see Ramsay and only refrained from punishing Ramsay for killing him due to the taboo against kinslaying. Ramsay may have let his manservant Reek die, but his obsession with making a helpless captive into another Reek speaks volumes.
Double subverted with Cersei Lannister, whose main motivation besides the sheer lure of power is the desire to protect her children since it was prophecised that they would die before her. There are many indications that Cersei is genuinely so deeply dedicated to her children that she fears seeing them die more than she fears dying herself. Unfortunately, her psychopathic idea of what's best for them, and her fawning on her even more psychopathic eldest son, is disastrous for the entire kingdom.
Both subverted and played straight with Tywin Lannister. Tywin is borderline abusive to all three of his children in varying ways but genuinely close to his brother Kevan and sister Genna. Genna says it best:
"How could I not love him....That is not to say that I approved of everything he did or much enjoyed the company of the man he became, but every little girl needs a big brother to protect her, and Tywin was big even when he was little."
How much various Lannisters love their family members is a pretty reliable barometer for how redeemable they're going to be. Most readers are willing to forgive Jaime and Tyrion for whatever they get up to, because they genuinely love each other, Myrcella, and Tommen, and try to do right by the other members of the family as well. Tywin's close enough to Joanna and Kevan that we at least feel something when he dies. Cersei almost becomes sympathetic early on when she's trying to protect her children from being killed as abominations (since they're the product of brother/sister incest), but then she turns on Tyrion... and Jaime... and Kevan... and Tommen... and, well, no one's going to be feeling much sympathy for her any time soon.
Averted with Gregor Clegane, who straight-up murdered most of his family (father, little sister, and at least two wives), earning him the undying hatred of his younger brother Sandor. Inverted with Sandor himself, whose hatred of Gregor is part of what makes him such a compelling character.
Sandor does play this straight-ish with his Morality Pet Sansa Stark, whom he kicks several times. However, Sandor protects Sansa and treats her with more compassion than he ever shows anyone else.
Joffrey is a vicious Royal Brat, but he seems to love his father Robert though he's unaware he's not really Robert's son. His cruelty is partly a misguided attempt to earn his father's approval.
In the Star Trek: Enterprise Relaunch, Admiral Valdore cares little for the appalling loss of life in the war of aggression he's waging. Indeed, despite some slight disquietude he shows little restraint in using near-genocidal tactics against Coridan. However, his love for his wife and children is always shown as completely genuine and admirable.
The protagonist of the Villain.net series is a kid named Jake. First the idea of being a supervillain seemed like fun, but when it costs him his family, he decides that becoming the greatest supervillain in the world is the only way to get them back, or else the only way to exact revenge.
Sunlight Gardener and Morgan Sloat in The Talisman genuinely love their sons. However, Sunlight's child is a psychopath in one world and a mutated freak in the other and Morgan Sloat's twinner's son died years ago. He does not care about Sloat's son at all.
Horris Quaiche from Alastair Reynolds' Revelation Space goes from Loveable Rogue to insane religious leader and dictator, but he genuinelly loved his tragically deceased lover (whose death triggered his descent into madness in the first place).
In Mortal Instruments, the Big Bad Valentine seems to actually care about Jace. That doesn't stop him from killing Jace. He is sad afterwards and tried to keep Jace from forcing him to, though.
He also seems to care for Clary, Jocelyn, Sebastian / Jonathan and Luke in his own twisted way.
ThaddeusValentine from Mortal Engines has his daughter Katherine who he truly loves and cares about. When she throws herself on Valentine's sword to protect Hester, he is heartbroken and dies cradling her body as London blows up.
In Animorphs,Visser One is pushing for a slow, secret conquest of Earth instead of the violent conflict Visser Three favors. An open war could result in the death of billions, and that might include the two children she gave birth to through a previous human host.
There's also David, who betrayed the team in part because they failed to save his parents from the Yeerks. He initially planned to ransom the Blue Box in exchange for their safe return.
In The Alien, a minor Yeerk agrees to help Ax assassinate Visser Three because the Visser's Kandrona rationing allowed the death of another Yeerk whom he was close to.
Tigerstar, the Big Bad of Warrior Cats had a mate and kits. So did his brutal, Blood Knight mentor Thistleclaw, and the eventually villainous Antpelt (minus the kits for him).
The end of Torch of Freedom produced plenty of this for the villains. They count themselves lucky that they and their families weren't in Green Pines when the nukes went off, but many people they knew were. Collin Detweiler mentions taking his children to a memorial service. That said, Green Pines itself was a genuine act of terrorism, which the heroes condemn as well.
A more extreme example is when Albrecht comforts Aldona Anasimovna after informing her that her mentor, Isabel Bardesano, was killed when would-be defector Jack Mc Bryde took out the Gamma Center (and he WAS working with the heroes).
Touched on and subverted with Ysanne Isard, Director of Imperial Intelligence and Big Bad of Michael A. Stackpole's entries in the X-Wing Series. In Isard's Revenge, she reveals that she was in love with the Emperor. Corran Horn believes she was in love with his political power, not the man himself.
In Wraith Squadron some of the Wraiths kill an officer about to shoot them, and ask the surviving officer for the code. When she's threatened she gives it up. "Sakira. It was his daughter's name."
The Fire-Us Trilogy sees the man who caused a near-total extinction of everyone in America (and very probably the entire rest of the world) sport a genuine love for his wife and two sons as the only redeeming part of his otherwise total evil.
Luke Castellan from Percy Jackson and the Olympians seemed very reluctant to hurt his former best friends (and possible love interest(s)) Thalia and Annabeth, even offering them to join the Titans with him. Throughout the series, he tends to tell his mooks to kill them all except Thalia and/or Annabeth, showing he possibly still cares for them.
And this is what leads him in the end to question his villainy and defy the Big Bad when he realises he accidently hurt Annabeth, leading him to be the one to save the world in the end. Redemption Equals Death.
Caine Soren from the GONE has no problem throwing innocent children off cliffs, but he gets outright murderous when anyone (or mostly Drake) hurts or even insults Diana, who he has stated twice to love and care about.
In fact, all the Coates kids have something or someone capable of humanizing them... Except Drake, that kid became a part of Jumping Off the Slippery Slope a long time ago and is proud of it.
Lord Raith from The Dresden Files instills this into his children to make them easier to control, but it kinda backfires on him when his eldest and most powerful daughter found out that he didn't actually give a damn about them himself. Then there's Warden Morgan, who is portrayed as an antagonist for the first few books but sacrifices himself to save his true love- and the reputation of the White Council.
Mab and Titania, on the other hand, turn this into Even Neutral But Scary Psycho Fae Queens Have Loved Ones.]
Nicodemus and Tessa both care about their daughter Deirdre (though Nicodemus expresses it very creepily) in spite of their collaboration with fallen angels and centuries of evil deeds. In Skin Game Tessa tries to foil Nicodemus' plan because she knows it will require Deirdre's death, and Nicodemus loses it when Harry taunts him about how he killed his own daughter to complete the plan. Afterwards, the long estranged Nicodemus and Tessa apparently have a reconciliation where they, united in grief, try to work through it together by burning their enemy's family alive. They are still very evil.
Legacy of the Dragokin: The Kthonian knights think of everyone else as worms to be squished but consider each other family. Their leader is Kthonia's daughter and her desire to free her is as much a daughter's love as it is a villain's Evil Plan.
Invoked by Johanna Mason in Mockingjay when she points out that if they hold a final Hunger Games with children of the people who held power in the old regime, President Snow's granddaughter will be eligible for the reaping.
Earlier, in The Hunger Games, there's Cato's grief-stricken reaction to the death of his district partner Clove.
The Mafia don in Dean Koontz's Darkfall is almost a parody of this trope; he is a professional murderer, openly calling Dawson and Rebecca "freaks" for their incorruptibility, but he is absolutely heartbroken that some hellborn monsters have killed his "doggies."
The Behemoth in Devils Cape is a superstrong, brutal murderer, but when he finds the dead body of his friend Hector Hell, he is furious and comes bursting out into the ongoing battle seeking revenge. There's also Scion, Hector's killer, who despite working for his uncle and the Robber Baron as an enforcer, helps the heroes stop the Cirque d'Obscurite when his uncle goes against the one thing Scion demanded as his price - that his uncle leaves his brother and father out of everything.
Many of the terrorists have family members who can be used against them, particularly when their love of those people is greater than their loyalty to the mission. For example, Jack breaks the initial Big Bad of Season 2 by pretending to kill his family, and Dina Araz of Season 4 cooperates with CTU to guarantee the welfare of her son (while pointing out that if he dies, she doesn't care whether the US gets nuked.
Lilah: Is everything alright? Are they taking care of you? - No, mom, this is Lilah. You called Lilah. Do you need anything? Do you need money? - No - mom, I can't come over. I'm in Los Angeles. You know that. - Don't cry. Mom, please, stop it.
Lindsey is wooed by Darla, to the point of confessing he wouldn't "mind" if she were the one to kill him.
Bester tries to play this card with Garibaldi in an early appearance, portraying himself as just a misunderstood family man. Garibaldi isn't having any of it. Later, it comes out that Bester really does have a true love: his mistress, a rogue telepath who ends up being abducted by the Shadows to become part of a Shadow vessel's Wetware CPU. Bester does not handle this well.
While Londo Molari's level of "evil" is largely dependent on which scheme he's embroiled in at the moment, and he's willing to lie to anyone and cheat every system in the book to get what he wants, it's clear that he cares for at least two people. Vir, for all the grief he's given, is a close friend and confidant as well as his eventual successor as ambassador. The other is his one true love (coincidentally, not one of his three insufferable wives) Lady Adira, for whom he goes FAR out of his way to please and who genuinely loves him in return. Considering the conniving, amoral people that make up the Centauri government, it doesn't end well for her.
Rodrigo Borgia may be, essentially, the pope as a mob boss, but he loves his children. To a fault, in fact. His physical affection for his mistresses is a bit more changeable, but it's clear that he cares deeply for both Vanozza (the mother of his children) and Giulia (his current lover).
Cesare's brother Juan, however, has no such compelling qualities. The only sympathy he ever elicits is the physical pain kind, after contracting VD after sleeping with too many whores.
In an antagonistic subversion, (she isn't 'evil' per se, it's more her avaricious brother, but she is still on the 'bad' side of the series by opposing the Borgia papal states) Catherine Sforda cares deeply for her only son, but even more deeply for her people. When she is besieged by Juan Borgia and he tortures and threatens to kill her son if she does not lower the gates, she is at first conflicted, and wavers between surrendering and fighting while receiving counsel from her lieutenants. In the end she memorably hikes her skirt at Juan and defiantly tells him she may lose her son but she can always have another, and he has far more to lose by going through with the act than she does. Her son seems to both despise and respect her for this as their love for one another cools, but does not dissipate entirely.
Breaking Bad: A recurring theme. Walter himself is a villain precisely because he has loved ones. The Salamanca family is seemingly completely devoid of any morality at all beyond devotion to family. Mike will kill anyone without batting an eyelash but is a doting grandfather. Even Lydia worries less about actually dying than that her daughter will think she abandoned her if she just disappears. note Although in many cases, the loved ones would probably be far better off if their providers weren't involved in the drug world to begin with.
If you hurt the Mayor or Faith, expect the other to come looking for you. The Mayor also loved his late wife Edna May.
Spike genuinely loved and cared for Drusilla, in stark contrast to Angelus, Darla, and Drusilla herself. Indeed his Establishing Character Moment has him instantly switch from threatening his future mooks to worrying about whether Drusilla is cold after she had wandered into the room.
Drusilla loved Spike (and Angel), if not with the same level of devotion that Spike had for her. Drusilla herself said it best.
"We can, you know. [Vampires] can love very well, if not wisely."
Angelus, however, is completely incapable of love, despite him and Darla being passionately evil, they both have ditched each other or ratted the other out at times in the past, just so one of them doesn't get killed, leaving the other to face the wrath of their pursuers. Angel, on the other hand, clearly loved Darla. As a human, it terrifies her, as a vampire, it sickens her.
Angel encounters a vampire couple who show this for each other while he's dealing with the news that Buffy has died (again). After Angel stakes the woman, the man turns himself into an unstoppable killing machine (with a very short lifespan) for a shot at vengeance. Angel ends up feeling guilty because his months of brooding over Buffy seems to pale in comparison to the love this completely evil monster felt for his mate and his reaction to her death.
The Master viewed his particular high-ranking minions like Darla, Collin and Luke, as his "children", and nearly loses the will to carry out his plans after Darla is staked.
Vampire Willow loved Vampire Xander. When she runs into the real deal and mistakes him for her world's version, she hugs him and jubilantly exclaims, "Xander! You're alive!"
Burn Notice: One episode has Michael do this once: Brennan the arms dealer is back for revenge, and he's holding Michael's brother hostage to get him to do his bidding. Michael is forced to comply, all the while surreptitiously contacting Sam and Fiona to try and find something they can use to make Brennan release his grip. In the end, Michael strings together the clues they find and figures out Brennan's weak point: he bluffs Brennan into thinking he's got an assassin positioned in Europe to kill his beloved daughter.Brennan is shocked that Michael would pull such a dirty trick and surrenders.
Charmed: Zig-Zagging Trope: Cole mentions that evil cannot love, yet he himself has some evil inside him and has loved Phoebe. There are also demons and darklighters that have fallen in love with mortals.
Chuck: Volkoff shows some hints of really loving his daughter Vivian. It's not mutual. He also has a loving mother, although since his personality was re-written, he doesn't know about her.
The City Hunter: Each of The Five have family and loved ones they want to think well of them, the best example being Kim Shik-Jong, who opts to attempt suicide rather than drag his son down as well.
Criminal Minds: In one episode called "Parasite", a conman who uses romance as one of his main weapons to trick people out of their money suffers a psychotic break. He may have been a cheating murderer at that point, but he did genuinely care about the safety of his wife and son. This same episode also made this a Deconstructed Trope; the profile notes that he cared for his family because he saw them as extensions of himself and his own achievements, rather than independent people with real feelings.
Dexter: A lot of the killers are shown to have families and friends they care about.
Dexter says he has no feelings, but grows quite attached to his family and some of his coworkers, and has other romantic relationships later in the series.
The Ice Truck Killer is revealed to be Dexter's brother, reached out to him so they could reunite, and wants them to kill Debra together. Dexter can't do it because he loves Deb, and tearfully kills Brian.
Miguel Prado loved his brothers, and is particularely broken up about Oscar's death. When Dexter tells Miguel that he's responsible right before garotting him, he is particularely enraged.
Subverted Trope with Trinity. Dexter discovers to his surprise that he is a dedicated family man and a pillar of the community, but it's later revealed that Arthur terrorized his family, and all but completely ignores his oldest daughter.
Also subverted with Jordan Chase, who is hinted to care somewhat for Emily, the woman he had his friends gang-rape years before, but ultimately has zero compunctions about murdering her when he has no use for her anymore.
Travis Marshal is shown to have a deep bond with his sister, but she ends up killed by his evil personality.
Ukrainian crime lord Isaac Sirko pursues Dexter for killing his friend Victor, also his gay lover.
Downton Abbey: One of the series' main villains is Lady's Maid Sarah O'Brien, a cold, stern, morally defective woman who shows herself to be capable of a variety of petty, manipulative and downright deadly actions as the series has progressed. However, in series 3, her nephew Alfred Nugent arrives at Downton — a bumbling naive character who O'Brien manages to blag a job and defends to the hilt, despite his clear lack of experience. Her sense of family duty towards Alfred is the defining factor that causes a huge rift between herself and her previous partner-in-crime, the scheming footman Thomas Barrow.
Doctor Who has the Slitheen, an alien crime family who we see mourning each other even while they're trying to irradiate / blow up Earth.
Firefly: Token Evil Teammate Jayne, a greedy mercenary, is revealed in "The Message" to have a mother and little brother (the latter of which is implied to be an Ill Boy) that he sends part of his earnings to. His mother sends him back The Hat.
Flashpoint: In this Canadian drama show, one episode has a drug lord begging the man holding a gun to his fellow drug lord...and brother.
Glee: Sue Sylvester's genuine affection for her sister.
The Good Wife: "Waiting for the Knock" has one of Lockhart/Gardner's major clients, drug dealer Lemond Bishop, under threat of arrest by the FBI. He's more worried about what happens to his son if he goes to jail than jail itself.
House of Anubis: Victor Rodenmaar, despite having had antagonized and pushed Sarah Frobisher-Smythe towards revealing a secret she didn't know, the two were very close childhood friends and he reacted with genuine grief when she died. He also reacts very strongly when anyone mention his deceased father in a negative light.
The rural Kentucky villains provide numerous examples of this trope. In season two, Mags Bennett used her three sons as henchmen and showed great warmth toward her adopted daughter, Loretta. After the deaths of Coover and Doyle, Mags killed herself by drinking poisoned moonshine.
In season three, Boyd's criminal enterprize includes his cousin Johnny and his girlfriend Ava, to whom he is very loyal.
Also in season three, Detroit mob lieutenant Robert Quarles has a wife and children back home. Quarles makes a point of talking to his son on the phone and mailing him postcards during his exile in Kentucky. Later in the season, however, as Quarles' schemes unravel and he plunges deeper into Oxycontin addiction, he ignores phone calls from his family. After the Detroit mob cuts ties with Quarles, Duffy suggests that Quarles go home. Quarles says that he has nowhere to go, suggesting that things may not be rosy at home.
Law & Order: In the first-season episode "The Secret Sharers": The victim was a drug dealer and paroled rapist who was believed to have been murdered in retaliation for raping the murderer's girlfriend. His parole officer said that he was one step over a slug. Yet he regularly gave money to support his young daughter. One of the detectives said "Hey, you think he's crap? I think he's crap!...but he had a little girl who thought he was Mister Rogers."
Law & Order: Criminal Intent: One villain was a con artist who had a mark's son murdered just to advance his scheme to defraud her. However, he did deeply care for one other person besides himself: his partner. Goren ended up exploiting his desperation not to hurt her to force a confession:
Eames: True love. Probably his only redeeming trait.
Legend of the Seeker: A D'Haran captain in "Deception", who's used magical weapons of mass destruction to massacre entire villages and praises Richard's willingness (disguised as a D'Haran) to do the same, is shown bringing food from army supplies against regulations to his family, whom he obviously loves.
In LOST, the main (sort-of) villain Ben Linus goes Papa Wolf on Keamy after he [[spoilers: kills his daughter]]; fortunately for the protagonists, this starts him off on his Heel-Face Turn
NCIS: Rene Benoit, aka La Grenouille, the Chessmaster target of the entire preceding season's Long Game sting operation, is the father of Jeanne Benoit. Also Ari Haswari, who was Ziva's brother.
Once Upon a Time: Regina/The Evil Queen loves her adopted son, Henry, and also her father (who was also named Henry). Mr. Gold/Rumplestiltskin cares deeply for his love, Belle, and also his son, Baelfire. He created the curse in an attempt to find the latter in the Land Without Magic. Captain Hook also loved Milah, and was devastated when she was killed. And despite everything, it's revealed that Cora genuinely loved her daughter, Regina.
The Dark Curse, which is the curse Rumplestiltskin created to find Henry, and is considered darkest magic in the show, is based on this trope. One of the ingredients for enacting it is the heart of the person you love most
Power Rangers Time Force: Ransik, the Big Bad, genuinely loved his daughter Nadira despite being a mutant terrorist. This is what causes him to be one of the very few Power Rangers main villains to find redemption. Even better, it's Redemption Earns Life. For the record, Ransik was winning his final battle with the Rangers. He was delivering a Curb-Stomp Battle such as had never seen before in the entire franchise when he realized that his daughter had been wounded in the crossfire. He immediately surrendered to prevent her from being hurt further.
The Prisoner: This turns out to be a big part of Number Two's motivation in the remake. Two loves his coma-stricken wife. Too bad she's secretly the real Number One. Her coma is powering the Village (which is actually a Dream Land) and it will be destroyed if she ever wakes up for longer than a day.
In "The Plague Dogs", Ray Kinsey loved his daughter Lilah more than anything else. But then, she stepped on a nail, got tetanus, and he could only watch helplessly as she died. Even worse was the fact that they had medicine, but raiders had taken it all away. Ever since then, he lost his sanity, trained a whole group of attack dogs, and will not be kind to any trespassers.
General Sebastian Monroe, despite being the big bad guy, does have loved ones. He was quite broken up over the deaths of his family, as "Nobody's Fault But Mine" shows in a flashback. He latched on to Miles, but it turned into a borderline erotic obsession. In the episode "Home", he was able to form enough of a connection to his old girlfriend Emma that he was quite upset over her death. That, and finding out that she gave birth to his son and sent him away to somewhere else left a strong impression on him. By "The Dark Tower", he is on the run from Tom Neville's coup and he will have plenty of time to try to locate his son.
Salem: Anne is the apple of her father's eye-his cold-blooded, murderous, eye. He even gives her an amulet that has anti-witch magic to protect her from members of his coven, though she just thinks it's a pretty necklace.
Played with in the episode "Deadman Switch". Bounty Hunter Aris Boch claims that he's working for the Goa'uld System Lord Sokar in order to possibly trade a particularly valuable target for the freedom of his family. His target, a Tok'ra operative, reveals that Boch has no family. Then it turns out Boch is a Punch Clock Villain who hates the Goa'uld just as much as our heroes, and Teal'c convinces him to fake his own death to allow SG-1 and the Tok'ra to escape.
Despite being Always Chaotic Evil, some of the Goa'uld actually seem quite fond of each other (Apophis really seems to care for his wife, Amonet, and son, Klorel.) Given their roots in mythology, lots of family relationships are far less loving. At the same time, Apophis did not much care about his brother Ra, using Ra's death as an opportunity to muscle in on his territory. He also has no qualms about killing Ra's son Heru-ur, his own nephew.
Adria is an interesting example. She's the Dark Messiah of the Ori in the 10th season and she's just as ruthless and villainous as one might expect given that pedigree. However, she does retain an affection for her mother, though it never quite becomes her downfall as Vala hoped.
Gul Dukat has a half-Bajoran daughter, Tora Ziyal. He goes insane(er) with grief when she is killed.
Cardassians in general are subject to this trope, as Cardassians are generally polite, considerate and loyal. It's just that they also happen to be loyal to a power-hungry fascist government. In one instance, we see a Torture Technician being visited by his daughter while he is at work, and offering her kindly fatherly advice on how to care for her pet. Right in front of the man the father is currently tasked with breaking.
A subplot in the novel Star Trek: Ship of the Line has Picard being sent back to Cardassia Prime to confront Gul Madred. Madred is glad to see Picard back and is looking forward to finally breaking him. Then comes in Worf with Madred's daughter (now grown) and a sphere that has a countdown timer. Picard reveals that the Klingons use this to test their courage. On the count of 0, deadly nerve gas is released by the sphere. Madred relents and agrees to help Picard liberate POW camps. Then his daughter reveals that she was the one who contacted the Federation and asked for their help. Turns out her visit to "Daddy's work" during Picard's "interrogation" has resulted in a Heel-Face Turn. Even more crushed, Madred even gives Picard ships to move the prisoners. Everything Kozara does in the novel is to make up for the dishonor of his defeat at the hands of Morgan Bateson and the USS Bozeman during Kirk's time in order to restore his son's honor. However, when he's beaten by Bateson yet again, he realizes there's no shame in losing to a better man. He also realizes that his son is a brat who only cares about himself. Bateson offers to tell the Klingon High Command that Kozara fought bravely.
Seems to love playing with this trope. In some cases, the monsters are monsters BECAUSE of what happened to their loved ones previously at the hands of other monsters or hunters, and some actually form close-knit "families".
In "Two Minutes to Midnight", Pestilence is hinted to have some affection for the demon accompanying him when he hugs her. He also cares a great deal about his brothers, the other horsemen.
Azazel reveals that his Co-Dragons Meg and Tom are his children (whether this means literally or not is unknown) and is furious when Tom is killed and Meg is sent back to Hell. Subverted Trope however when Tom tests the Colt on Meg without batting an eye. Meg at least seemed shocked that her "brother" would do this to her.
Lucifer wants to wipe out all humanity and the demons and turn the Earth into his own pristine Paradise. He does show affection for angels though, especially his three direct brothers, the other archangels. He begs his younger brother Gabriel not to turn against him and is on the verge of crying when he has to kill him. His reunion with Michael is filled with mutual regret over what happened in the past and Lucifer again tries to convince his older brother to stop fighting each other. Subverted when Gabriel and Michael both point out that he loves himself even more and is only going on a petty temper tantrum against God for creating humans, although his affection for his brothers appears genuine.
Subverted Trope when it's discovered the demon Crowley had a son, Gavin, who they were sure could be used as leverage against him. Turns out they both despise each other. Crowley proclaims he couldn't care less what they did to Gavin and that he would even relish the idea of them tormenting his soul. His son then gets him back by betraying the location of Crowley's bones in hopes they could burn them.
Terra Nova: From Boelyn's point of view prior to Lucas Taylor taking over Terra Nova, Nathaniel Taylor fits this trope:
Boelyn: Taylor's a complete bastard, and then some...but he loves his son. He'd sooner slit his own throat than hurt Lucas.
True Blood: No matter how vile, depraved and generally awful any given entity (supernatural or mortal) may be, they tend to have at least one person whom they truly, deeply love. Even the likes of Russell Edgington had his beloved Talbot.
Veronica Mars: Aaron Echolls physically abuses his son Logan, cheats on his wife, and murdered a teenage girl that he slept with after she threatened to tell on him, but he cares a great deal about his adopted daughter Trina. Enough to unleash a severe beating on her abusive boyfriend when he finds out what the guy did to her.
In the ever-confusing plot surrounding Samantha Mulder and whatever became of her, at one point it is said that the Big Bad, CSM, rescued Samantha from her captors and raised her as his own. She points out that he was a caring and loving father.
For that matter, CSM's "complicated" relationship with Mulder makes more sense when it's revealed that he is quite possibly Mulder's biological father.
His son Jeffrey Spender, on the other hand, appears to receive far less regard, ending with CSM permanently disfiguring him.
Ingrid is excited to become evil incarnate by joining with her blood mirror self, but draws the line when it suggests she kill her boyfriend Will and decides to run off.
He won't admit it, but the Count still has feelings for his ex-wife Magda. He does sometimes show that he cares for Vlad as well.
Slim Shady is entirely amoral, and loves his daughter.
Gorillaz: His exact motivations are unclear, but Murdoc seemingly panicked and rushed to help when discovering that the real Noodle was alive and under attack by pirates. It can't be just for the sake of the band, because he still has Cyborg Noodle, which he used to make the Plastic Beach album. Real!Noodle served as his Morality Pet before her disappearance, so...
The Bible mentions this to make a point: If evil people know how to give good gifts to their children, then how much more does God know how to give gifts to His? Also given as one of the reasons we are supposed to love our enemies: Even evil people love those that love them, so there is nothing really extraordinary about loving those that love you.
The Song of Deborah has an interesting example when, amidst celebrating the evil general Sisera's defeat and death, Deborah imagines Sisera's mother anxiously waiting for her son to return from battle. The contrast is reversed again when someone consoles Sisera's mother that her son is probably just late because of all the Israelite women he and his men are raping.
Warhammer 40,000 has the infamous relationship between Nurgle, Chaos God of Disease, and Isha, Eldar Goddess of Healing. It's kind of one-sided, but it's the closest to nice that a Chaos God can ever get.
More generally, this is Nurgle's relationship with all his worshipers. He genuinely loves everyone, even his enemies, and will offer comfort and succor to all who suffer the travails of the condition of being mortal. That said succor involves making a person comfortable with the idea of decaying into a bloated and twisted form for however long they may last, and that refusal will result in his followers battering a person until they accept Nurgle's love is irrevelant to the affection he feels for them.
Warhammer: Warriors of Chaos has a character named Valkia the Bloody. She has a rule called "Consort of Khorne"; it lets her reroll on the Eye of the Gods table if she doesn't like the results. The reason she can is because her patron god, Khorne, who went so far as to resurrect her following her first death, can't stop watching her. This is a god whose throne is made of Nothing but Skulls.
Valkia had a great deal of attachment to her late father.
The Order of the Stick: Rich Burlew covered this as a way to make villains more fleshed-out in his Villain Workshop articles. In the presented example, two villainous siblings were honestly planning to divvy up the world between them and rule without fighting each other, but the heroes believed Evil Cannot Comprehend Good and assumed they were both gearing up to backstab the other. This led to a very shoddy attempt to play one side against the other that failed in the worst possible way.
On an imperialistic note, this is how the Ur-Quan in Star Control function. The two warring religious sects decided to have an amicable split and fly away from each other until they conquered their half of the galaxy, then turn around and begin the battle again. One of the major plotlines of Star Control II involves the more violent sect having been the one to finish their goal first.
Titus Andronicus has the titular character as well as Tamora and Aaron, all of whom love their respective children, or are at least willing to kill anybody who lays a hand on their respective children.
Claudius in Hamlet genuinely loves Gertrude, enough to kill his brother for her. He actually also seems rather fond of Hamlet, before Hamlet reveals that he's on to him.
Apparently, Arl Howe is this, too. When you meet his son Nathaniel in Awakening, he plans to kill your PC for murdering his dear dad. Nathaniel, though, didn't know exactly what his father was up to when he wasn't with his family.
Though you may debate whether anyone in Dragon Age II is really 'evil' due to the omnipresent Grey and Grey Morality, even if you play Hawke as a dog-kicking madperson with a tendency to let dangerous blood mages go/sell out innocent mages to the Templars when all they wanted was a taste of freedom, he/she still cares about his/her family.
In Warcraft III and especially the addon The Frozen Throne, Illidan has long been over the fact that Tyrande ended up with his brother Malfurion. Even though he was imprisioned by Malfurion for 10,000 years, exiled from his homeland, and sentenced to death for his repeating dealings with demons, and their armies have often fought against each other, Malfurion more than once accepts Illidans offers to ignore their own history when offered his help to save Tyrande. Though his title as a demon lord is The Betrayer, he never has any hidden motives in these situations.
In World of Warcraft, Sally Whitemane turned to extremism after losing her family to the Scourge. After she's defeated in the updated Scarlet Monastery instance, she calls out "Mograine...", the name of her comrade in arms and possible lover, who was killed in the Ashbringer comic series.
Shannox, in the Firelands, gains a damage buff when you kill each of his hounds, and expresses his outrage toward the raid.
Alex in the Bastard of Kosigan series has definitely crossed the Moral Event Horizon, but her dialogue hints that she still loves the player.
Neverwinter Nights 2: Mask of the Betrayer might not count as Akachi isn't technically a villain, but his love for the Red Woman and his brother do help bring him back to himself and end the curse that is killing your player.
Araman himself still loves his brother and has a tendency to not attack you when he really ought to.
Overlord has the title character gain a mistress partway through the game. Rose is prim and a bit condescending... although even later in the game, you can dump Rose for her sultry sister Violet. It turns out that both girls are the daughters of the former Overlord and the one you didn't pick will betray you when her father returns. As the sequel shows, the Overlord stayed loyal to Rose.
Overlord II stars the son of the previous Overlord, after said Overlord vanished at the end of Overlord: Raising Hell (while his mistress was pregnant). He has one childhood friend Kelda, who in turn becomes his first mistress. Even in the stage of the game when both are children, Kelda is the only character who likes the Witch-Boy and doesn't treat him like the Enfant Terrible he is, instead trying to protect him from bullying while developing a crush on him.
Present among Dark-Side characters who choose to partake in a Romance Sidequest in Star Wars: The Old Republic, but it's especially notable for the Sith. Dark-sided Warriors are typically ruthless, bloodthirsty, intolerant of failure, and quite possibly cannibals; dark-sided Inquisitors are typically Magnificent Bastards and Social Darwinists who love electrocuting people and take sarcasm to Jerkass levels. This doesn't stop them from genuinely loving their chosen paramour.
In Castle Crashers, after you defeat the Conehead Groom a big, burly cyclops enters the scene, picks up the Groom's body, and cries. He then escapes with the Princess. When you finally catch up to him, he's holding a funeral for his pal. Whether the groom was his son, father, or just a good friend is unclear.
Throughout BioShock, it's implied that Andrew Ryan had an illegitimate child. Later, it's revealed that Jack himself is Ryan's illegitimate son. Fontaine kidnapped and brainwashed Jack to do his bidding precisely because he knew that as evil as Ryan was, even he couldn't bring himself to kill his own son.
The Panda King from Sly Cooper series has his daughter Jing-King, whose distress is the driving force of the third episode in Sly 3: Honor Among Thieves. He even joins up with the Cooper Gang for her sake.
Saints Row: The Third leaves it up to the player to decide whether the Boss cares enough to prevent Saints from being killed or whether they're just a convenient excuse for the next rampage.
Castlevania's Dracula genuinely loved both of his wives; it was their deaths that prompted him to go evil. Twice. In Castlevania: Symphony of the Night, he expresses remorse upon finding out that his actions go against his second wife's last words. He is also rather fond of his son Alucard, even though Alucard has sworn to oppose him.
In the Lords of Shadow continuity, Dracula's love for his wife and son is stated to be the only pure human emotion he has left.
In Alpha Protocol, Alan Parker is a cold and calculating person who considers everyone he works with as expendable and has no problems with eliminating them if he sees it as necessary. However, with enough research, Mike can find out that he's the father of Madison Saint James. If Madison is killed by Conrad Marburg, Mike can inform Parker of the man who killed his daughter, which will result in him trying to take revenge, or at least try to.
In Mass Effect Renegade Shepard can be played this way (though it’s more Anti-Hero than evil). S/he can kill civilians and hostages because it makes his/her job easier, backstab his/her allies, execute enemies on the spot (often in rather painful ways) and be a jerk. But at the same time s/he can be shown to care deeply about one or more of his/her squadmates and beat the shit out of people trying to harm them.
Chapter 8 of Valkyria Chronicles largely serves to humanize the imperials when the the two leads are separated from The Squad. They attempt to nurse back to health an injured enemy Mook, who dies crying out for his mother, and later while thanking them for their mercy, his commander mentions the wife and daughter he has waiting back home.
In Fallout 3, killing the Overseer (Alphonse Almodovar), either during "Escape!" or "Trouble on the Homefront" if you didn't do it the first time, results in Amata calling you outfor killing her father and only living relative. In Broken Steel, one of the scientists at Adams Air Force Base has a holotape from her brother that says he was transferred to the Satellite Relay Station, where he was likely killed by either the Lone Wanderer or the Brotherhood. Furthermore, in Fallout: New Vegas, it is found out that ED-E was built by an Adams AFB scientist named Whitley, who was also probably killed.
The Big Bad of Radiant Historia. The biggest obstacle stopping Heiss from completing his "destroy the world" objective is the fact that he really, truly cares about Stocke, and a large part of his plan is an effort to save his life and train him to take over. Right up until the end, Heiss is unwilling to seriously try to kill him because he's still holding out hope he might change his mind, and in the True Ending, he ultimately decides that if one of them has to die, it's going to be him, not his nephew.
In Assassin's Creed III, Haytham Kenway genuinely loved Ziio and their son Connor. Sadly, his dedication to the Templars was stronger.
In Blip, Incubus and Succubus care for each other; their loyalty to each other is stronger than their loyalty to their boss. In fact, when Incubus was seriously injured, Succubus seemed willing to sacrifice herself to save his life.
In Evil Plan The Webcomic, supervillain Dr Kinesis still visits his clueless family for the holidays, and looks out for his sister, objecting to her fiance as any suspicious sibling might.
The Order of the Stick makes it clear that an "evil" alignment does not prevent a character from having loved ones.
This was especially clear in Start of Darkness, which subverts/inverts it when Redcloak does pick Xykon over his brother, and not because of Xykon's vision, but his own.
General Tarquin, Lawful Evil father of Elan, demonstrates this trope quite blatantly, celebrating his long-lost son's homecoming by throwing a festival that culminates in spelling out said son's name by burning escaped slaves nailed to the side of a mountain, while still alive. However, this is actually a subversion: Tarquin supports Elan because he wrongly thinks he's the Big Bad of the piece and therefore a legendary enemy for The Hero (Elan in his Wrong Genre Savvy way of thinking) to overcome, and kills his other son, Elan's twin Nale, on account of his belief that Elan has outgrown him as a recurring adversary.
Tarquin's right-hand Malack lost three offspring in a revolution. Even years later, he wants to be a father again but can't find another true love and is unsure about adoption. He loves children so much so, that he takes Durkon and bites him to turn him into a new one.
Enor and Ganji are fairly amoral, greed-driven bounty hunters who are willing to kill friends and family members of their collected bounties should they come asking. However, they truly do care for each other, which is another Kick the Dog moment when Tarquin orders them to fight each other in the gladiator arena, which he sent there because they "tried" to extort money from him by playing out another Star Wars reference in a long string of them.
Nale and Sabine seem to honestly care about each other, even though she's apparently keeping the secret about working for the Three Fiends from him.
The whole of the Linear Guild seem to be good friends and coworkers, to the point that Nale is willing to attempt to fight barehanded against a vamped Durkon to protect Zz'dtri.
The ancient black dragon was probably evil before she ever decided to avenge herself against Vaarsuvius, but she had a very specific beef when Vaarsuvius killed her only son. She also mentions her mate having been killed by adventurers. Vaarsuvius is shocked when s/he realizes the extent of damage she did with her Familicide spell. In particular s/he notes that the dragon who was the ancestor of the Draketooth clan had three children with a human woman, implying a stable relationship rather than a one-time fling.
One of the ways Tarquin controls his soldiers is by threatening their families. On top of that, however, at one point one of the soldiers is about to do something that will make Tarquin mad, and one of the other soldiers is quick to stop him to keep him safe. Even random evil mooks are friendly with each other.
In Goblins, the only remotely humanizing moment Dellyn Goblinslayer has is when he weeps over the mutilated body of his former comrade, Saral Caine.
In Homestuck, the Pre-Scratch Trolls' secretly Token Evil Teammate, Kurloz, still cares for his ex-matesprit, even though: a) His post-scratch incarnation is pure evil; b) He's not much different in his intentions, given that he worships, with his successor Gamzee, Lord English; and c) His successor brutally killed Meulin's successor, Nepeta. He's also moirails with Mituna Captor, meaning that it's Kurloz's job to serve as Mituna's emotional crutch, something Mituna defintively needs considering his psychically self-induced brain damage.
Gamzee himself could also qualify in regards to Calliope. During his interactions with her as a young child, she's shown to be quite the Daddy's Girl, and he has a genuine, non-psychotic smile on his face as he hugs her.
In Dragon Ball Z Abridged Jeice and Burter show tremendous friendship for each other. On the rest of the Ginyu Force? Over Guldo's death they were discussing the last time they masturbated.
Ginyu as well. He is shaken by Burter's death, calling it a hefty loss, Recoome's is what sends him out for revenge and after Jeice's he voices genuine distress, even pleading with his foes for a brief moment of silence of mourning.
Friendship is Dragons features Rainbow Dash as a Chaotic EvilinvokedBarbarian. When the GM argues that this means she doesn't fit the Element of Loyalty, Dash's player argues the point using this. Yes, she fully intends to do Evil and selfish things in the future, but that doesn't preclude her being faithful to her True Companions. She does what she wants, regardless of what others say, and that includes having friends she refuses to betray.
Worm has a couple examples. The supervillain Marquis cares deeply and sincerely about his daughter Amy, putting her wellbeing and happiness ahead of his criminal enterprises and his own life.
Similarly, the white supremacist supervillain Purity cares deeply about her daughter and goes out of her way to take care of her stepson.
A much creepier example is Bonesaw, an incredibly screwed up little girl who treats the other members of the Slaughterhouse Nine, a band of psychopathic spree killers, like a family.
The Dark from Brennus is the most powerfull supervillain in the world. He is also a caring father and a Benevolent Boss.
Tom Collins of Demo Reel has a girlfriend and treats his film company like his family. When they all leave him for acting like an obsessive ex with Donnie, he takes it out on Rebecca and Tacoma, destroying the movie they made for their friend.
Bronyism's Trollvorlord may wish enslavement and death upon the human race, yet he still cares for his best friend Noah/Troll King and (secret) girlfriend.
Lady Havoc was a Mad Scientist with a severe mental illness and a body count in the dozens. She had escaped from prison years before, and was on the run, all the while building weird science devises and going on rampages. Yet she risked everything to save her father's life from a terminal illness. Later, she made a deal to turn herself in if the local superheroes would help her save her younger brother from a sadistic supervillain who was holding him hostage... and kept her word afterwards.
Teshirock from Noob who turns out to have gone into his villainous activities in hope to restore communication with his estranged son in the first place. He also seems to care deeply about his guildmates from the time he was an actual player, to the point of still being on good terms with the one that turned to Real Money Tradeand asking his guild master to stop playing upon realizing that he has a mental condition that makes him a great MMORPG player, but can also cause an unhealthy level of addiction to the game.
Xanatos of Gargoyles is extremely protective of his son Alexander and loves his wife Fox (who herself wasn't exactly a hero). When Oberon asks them to give up their son, it does not go too well.
This also counts for several members of the Third Race, even if they tend to be more chaotic than straightforwardly villainous. Oberon and Titania clearly care about each other, and Titania also has a good relationship with her daughter Fox, at least before she started scheming. Puck, likewise, is an Honorary Uncle in the Xanatos family. The Weird Sisters, who may have been the real Big Bads of the series, considered Demona and Macbeth "our responsibility" and "our children" (or claimed to, at least).
Demona herself, who clearly loves her (heroic) daughter Angela—but unfortunately, this just gives her more rationalization for Killing All Humans.
In Teen Titans there was the case of Kitten and her boyfriend Fang.
Azula loves her father Ozai and is a Well Done Daughter Girl just like Zuko, albeit one who's used to getting the attention she craves. She also loves her mother, Ty Lee and Mai, though because of Ozai's teachings these feelings are twisted.
Iroh genuinely cared for his son Lu Ten and his brother's kids. However, he spends the series being a Cool Old Guy, so this only applies when he was the Fire Nation's foremost commander.
The Warden of the Boiling Rock values his prison's reputation above everything else, but he also loves his niece Mai he's angry at Zuko for breaking up with her, and when she facilitates an escape from his prized prison, and was arrested, he pulled some strings to help in her release.
This trope is the sole reason Zuko took so very long to perform his Heel-Face Turn. He loved his father and wanted nothing more than to return to when his family was happy together.
The two villainous brothers, Noatak (Amon) and Tarrlok genuinely care for one another in terribly warped ways, Noatak taking Tarrlok with him to restart his anti-bending regime as a family, and Tarrlok commiting Murder-Suicide to save his brother from himself.
And then there's their father, Yakone, who despite his cruelty ended up in a northern water tribe, with a wife who loved him just as much as he loved her.
Eska may not be very nice, but she still loves her brother.
Zaheer and P'Li's romance is very sincere and almost sweet. When she dies, he seems genuinely heartbroken.
Mr. Boss, from Codename: Kids Next Door, despite siding with Father and claiming to be a child-hater, has 3 kids of his own that he marks as an exception to his hatred. One of his kids is Fanny, a.k.a. Numbuh 86 of the Kids Next Door themselves, no less. In turn, Numbuh 86 also unconditionally loves her father, despite being one of the most militant, borderline Knight Templar KND agents.
And in "Planet of the Bikers", the Dominatrix Space Bikers turn out to be a respectable elementary school staff on their home planet, and the mention that one has a kid on the way even causes Jenny to D'awww.
Hoggish Greedly from Captain Planet and the Planeteers may be a supervillain, but he truly loves his son Junior. The one time his polluting put his son in harm's way, he performed an Enemy Mine with the Planeteers to fix it.
The first most prominent antagonist of The Grim Adventures of Billy & Mandy had Nergal who went on to marry Billy's aunt, Aunt Sis, and produce their son, Nergal Jr - Billy's cousin. He still remained a villain, but was considerably more easy on Billy and often spoke of his love for his wife.
Although his evil can be debatable, Dr. Heinz Doofenshmirtz in Phineas and Ferb deeply cares for both his daughter AND his arch-nemesis. For the former he spent years looking for a doll she wanted and the latter is Friendly Enemy; when Heinz isn't doing anything evil, they hang out in his suburban backyard.
The Monarch and his wife Doctor Miss The Monarch (formerly Doctor Girlfriend before she got married) are frequently considered the strongest, most loving relationship in the entire Venture Brothers show, even if they are deranged supervillains.
The X-Men: Evolution version of Mystique seems to genuinely care for her son, Kurt, despite trying to take out the rest of the X-Men.
Cybron from Skysurfer Strike Force has a very low list of morals being the show's Big Bad and trying to use his Bioborgs to take power by force. However, he loves his daughter Cerina so much, he practically begged the Skysurfers to save her.
Dreadwing is also bent on revenge when he finds out Optimus killed his brother Skyquake, and moreso when he finds out Starscream desecrated his corpse by raising him as a dark energon zombie. In the end, his loyalty to Skyquake's memory is greater than his loyalty to the Decepticons, and Megatron kills him to save Starscream.
It's hinted rather strongly that Soundwave cares for Laserbeak. When the drone sent him an S.O.S., Soundwave drops everything and leaves immediately to go assist it, even though there was absolutely no reason he couldn't have taken a moment to finish off Wheeljack first. He also seems to be friendly with Megatron, though whether it's actually friendship or a more professional sense of loyalty (and appreciation for that loyalty on Megatron's part) remains to be seen.
Predaking was the first Predacon clone made, and cares deeply for the Predacons to come after him. When his fellow Predfacons were destroyed before their lives could even begin, he swore a similar extinction on those responsible.
In The Transformers Season 3, the closest thing to Decepticons having loved ones is how Cyclonus behaves towards Galvatron, who despite all the abuse Galvatron dishes out to his Second-in-command, is undyingly loyal and seems to genuinely care about his Leader.
If friendship counts (though some fans like to read Ho Yay into it), Starscream's bond with Skyfire is an example. Skyfire is a walking relic of Starscream's youth, before he had committed himself to evil, and he's the only character we ever see Screamer act sincerely nice to. When Skyfire "betrays" Starscream by refusing to be a Decepticon, note Fandom tends to make a lot of the fact that Skyfire is a former Decepticon, ignoring the fact that his entire tenure as a 'con lasted maybe half a day, until he realized what the 'cons are actually like. the last vestige of decency in Starscream dies.
Abraham Kane, the Big Bad of Motorcity, has his daughter Julie. He doesn't know she's a Burner and the Burners don't know she's his daughter.
Most notable in the finale when Mike Chilton pretends to take her hostage.
In Adventure Time, we have two examples of this:
Hunson Abadeer is one of the most evil entities in the series (which is saying a lot considering this is Adventure Time we're talking about) and he was sad when he found out that Marceline still begrudges him for eating her fries by hearing the Fry Song.
Ice King has his penguin, Gunther, whom he always carries around with him, and more or less all the other Gunthers in the Ice Kingdom. Also, before he was Ice King, he had his fiancée Betty, who he always called his "princess" and was visibly and verbally heartbroken when he left her.
In Young Justice, Cheshire genuinely cares for her younger sister Artemis, even saving her life mid-battle. She even names her daughter after Artemis' middle name. In season two, it appears that Black Manta has grown to care for his son, Aqualad.
Futurama: "Whenever I said, "Kill all humans," I would always whisper, "Except one." Fry was that one."
Jimmy Two-Shoes: Heloise is the most competent villain on the show, but she still genuinely cares about Jimmy.
This gave him enough of a Guilt Trip that he hands the little girl some money out of his wallet to buy her father a present - so long as it's not a nail-file.
Wunschpunsch: Bubonic and Tyrannia might hate each other and have no qualms about casting evil spells (despite being usually too lazy to start before their supervisor shows up) but love their respective pets. Then again, unlike their book counterparts, they don't know said pets are the ones who ruin their spells.
On Justice League Unlimited, the Huntress is an Anti-Hero on a quest to avenge her murdered parents; the irony is that her father, while very loving to her, was a crime boss who was usurped by one of his own nastier lieutenants. She ultimately finds herself unable to go through with it when she discovers that the murderer has a young son whom he loves just as much.
In The Simpsons, Chester "Snake Jailbird" Turley might be one of the well-known criminal, often taking actions dealing with convenience stores thanks to Moe stealing Mayan coin Snake had found while working as an archaeologist and planned on given them to a museum, but he’s surprisingly a good father towards his son, Jeremy, even if it means sharing in his ‘current’ business.
Jeremy (riding away on a stolen bike): "I'm stealing, Daddy! I'm stealing!"
Snake (wipes away a tear): "That's my little dude…"
Darkly subverted in the Batman Beyond episode "Ascension". Derek Power's son Paxton initially seems concerned for his father's health and safety. Paxton later reveals that he purposely set up the protest by the Verdeza activists in order to expose his father as Blight. He then hired Batman to search for Blight pretending to plan to help him when he was actually intent on killing Blight and taking control of the company for himself.
Even though the eponymous dog in Mr. Pickles is a demonic psychopath who regularly kills people, frightens and/or has sex with other animals, and conducts satanic rituals in his doghouse, he seems to genuinely care about Tommy.
In The Little Rascals episode "Tiny Terror", even though Butch is a bully, he is fiercely protective of his baby brother.
...and when the hero launches into an explanation of morality that goes way over her head, that will be her cue to pull the lever and drop him into the pit of crocodiles. Children love crocodiles as much as evil overlords [do], and it's important to spend time with the grandkids.