Harara of Apocalypse Zero is an unusual villainous version of this trope, being wholeheartedly grateful to the monsters who serve him and concerned for their well-being. Yes, even though most of his servants are perverse, murderous mutant horrors. They, in turn, respect and idolize him.
At first played straight, then horrifically and utterly subverted with Griffith and his Band of the Hawk of Berserk. Yes, he did genuinely care for the people in his army, even going as far as to personally get to know them himself. However, after finding a dead child he'd grown attached to and suffering a Heroic B.S.O.D. (Which lead him to sell himself for one night to a pervertedBaron for money), he realized he had to emotionally distance from his troops, essentially reaching the point where he saw them more as tools than people. Well, except for Guts, that is.
Balalaika in Black Lagoon is a rather warped version of this. She actually was the commanding officer of her men when they were part of the Soviet military, and now that they're...no longer in the military, Balalaika's concern for her subordinates are her Pet the Dog moments. If you attack any of this Magnificent Bitch's men, you will be DEAD.
Note this extends to her part-time employees as well, most notably the Lagoon Company. She might be utterly ruthless, but her recurring Pet the Dog trait is her unswerving loyalty to her comrades, regardless of duration.
Dan Roana is a female example from Blade & Soul. She gets a lot of respect from her underlings because she looks out for them and usually has their best interests in mind. She tells Alka about it in episode 3, stating that they largely formed the group because they had no one else to rely on after they or their friends/relatives were attacked by Jin Varrel and Palam.
Played with in YuGiOh: As Pharaoh, Atem is younger than most of his troops, but he's fiercely protective of them and his people. At one point, he heads into a potentially lethal situation with little firepower because his soldiers would have been killed by Bakura otherwise.
Juushirou Ukitake is known for the great concern and strong emotional attachment he shows to his subordinates, and generally displays the most "fatherly" attitude of all the captains. He also feels deep personal guilt if one of his subordinates is hurt or killed. Even after many years, he was still unable to replace his fallen lieutenant Kaien Shiba until both he and Rukia were able to heal enough for Rukia to become his lieutenant during the 17 month time-skip.
Subverted: Aizen was very much this to his subordinates, especially towards Hinamori, Renji and Kira. Then he revealed he had been a Magnificent Bastard all along.
After the Soul Society arc, it's revealed that Byakuya's squad was incredibly proud of the fact that he had lived by the same law-obeying standards he preached to his men. When brutally defeated in the final arc, he admits to Ichigo just how much shame he feels that he did not have the strength to save his squad or even spare his squad's loved ones the grief of losing them. Later, when Kirinji asks him if he's well enough to regain his arrogance, Byakuya admits he's not and that he's got a very long way to go before he ever has the strength to regain his former arrogance.
Kirio Hikifune was supposedly like this when she was Captain of Squad 12, which is why when she is promoted to the Royal Guard, Hiyori has a hard time initially accepting Urahara as the new Captain.
Professor Zorndyke from Blue Submarine No. 6 applies in every interpretation of this trope. The literal creator of an entire army and race of chimeras, whose appearances range from adorable to nightmarish, Zorndyke is looked upon more as a father than a military power by his children. This feeling is mutual in that he cares for all his children and teaches them how to speak, read, and often prays for their safety. This relationship is often shown through his interactions with his son Zerg. As the series goes on we see that Zerg does everything in an effort to please his father and make him proud (He also never refers to him as anything else but "Papa"). Probably the crowning moment of this trope was at the end of the series were all of Zorndyke's children carried their father's body into the sea for burial. The moment is truly saddening and tear jerking, even more so when Verg appears, exhausted and dying from his own wounds, who upon seeing his father's shrouded body cradles him and cries like an child, screaming for his Papa.
Captain Tsubasa has Hikaru Matsuyama, both during his time in the Furano Junior High team, and in the national team. It's thanks to him and this quality of his that the national team doesn't crumble after the humiliating Curb-Stomp Battle at the hands of the Real Japan 7 team, the expulsion of the regulars, and the brutal Training from Hell from Coach Gamo in the World Youth Saga.
Being the captain of Japan and the titular hero, Tsubasa also displays this quality, albeit not as proeminently as Matsuyama.
Although she can be harsh, Sister Kate of Chrono Crusade genuinely cares for all of the exorcists under her command and often treats them as her children. In fact, she's generally portrayed as being harsh towards Rosette because she does care for her and is concerned for her.
Code Geass has Andreas Darlton, a Britannian general and part of Princess Cornelia's military staff. He's a Reasonable Authority Figure and the first Britannian to give Suzaku a fair chance despite his race, and even supports the young man's being knighted after he proves himself. The trope is also literal: Darlton adopted five orphaned soldiers, serving as both their commander and father figure, training them up to become the elite soldiers known as the Glaston Knights (who are, in turn, fiercely loyal to their "father").
Cornelia herself is a Cool Big Sister for her men, especially her bodyguard. He has a really hard time convincing her to run away and let him buy her time. Seriously if you watch this episode alone, it's impossible to figure Cornelia is the Big Bad.
General Tiedoll in D.Gray-Man. Kanda doesn't appreciate it at all.
The plot of Dorohedoro begins when the central character, Kaiman, kills a magic user. He does this every day, and in fairly large amounts, but this one was working for En, a major player in the Magic World, and he is very angry to find out someone's picking off his men. Later chapters show that En regularly treats his employees to various special events.
Dragon Ball: King Piccolo is the only villain in the entire series to give a damn about his underlings, going as far as to avenge them if they fell in battle. Helps that they are actually his kids.
Several of the Guild Masters display this trait in Fairy Tail:
Master Makarov treats his guild like his family, even referring to them as "my children" (one of them is his biological grandson to boot), and has gone Papa Wolf (along with two instances of attempted Heroic Sacrifice) when they were attacked.
Master Bob of Blue Pegasus seems to have a similarly fatherly relationship with his guild, offering concerned advice to its members.
Obaba of Lamia Scale acts like a grouchy old lady; but since very few people can compel mages as powerful as Jura and Lyon to do something, it's likely that they hold a lot of affection for her as well.
Major General Olivier Mira Armstrong from Fullmetal Alchemist. She and Buccaneer agree to a 24-hour time limit for him to search for the scouts lost in Sloth's tunnel, and the door is to be sealed even if they don't come back. It takes them over 24 hours to return since they douse the light to avoid getting attacked by Pride, but there's a door waiting for them because she gave the guy in charge of sealing it a broken watch and he knew what it meant. Also, in order to send his support team, she has no problem with shoving her superior into wet cement (and telling her men she'll take all the blame if anyone else ever finds out).
Mind, she stabs said General to death first, and there's also the whole plan to infiltrate the genocide conspiracy she'd just pumped him for information about.
It's worth noting that Olivier is a Social Darwinist, with a streak of General Ripper and only shows this tendency toward living or probably living soldiers. If the soldier is dead, he'll get last priority. "He's dead with a smile, so be it. We've got other pressing matters at hand."
Easily her equal in this trope is Roy Mustang. He endangers an entire operation to rescue two of his most loyal subordinates from certain death, even though he's the one who ordered the operation and if his activity is known, explaining it will be difficult and probably ruin the "ruthless careerist" personahe employs as cover. (For this, his personal aide - one of the two he rescued - calls him an idiot. But she's allowed.) There's a reason his old unit from the war comes back to help in the finale - as one of them says in a flashback, he went out of his way to protect them from harm, and they credit him with being the reason they all survived. He also recruited the Elric brothers prior to the start of the anime/manga - and because they are literally children, with a Missing Mom and Disappeared Dad, they are in some ways like his sons.
Don't forget Brigadier General Hughes. He's like a doting father-figure (or brother, depending) to the entire military, particularly Roy, Ed and Al, as well as a (somewhat nauseatingly) devoted father to his daughter, Elysia. Rest in peace, Maes Hughes. The Meaningful Funeral proves just how much everyone really loves him.
Though, mind, the only actual subordinates of his we see are Brosh, Ross, and Schezka, who find him terrifying, and a couple of people who think he's kind of annoying. So he was very hands-off about the nurturing thing.
If he was nice all the time, he wouldn't have been able to join the army in the first place. Sometimes being assertive is part of his job.
Ling Yao has many shades of this, though he's a prospective heir to the throne of his country rather than a military officer. He strongly believes that a king is nothing without his people and absolutely despises anyone who sees their subordinates as expendable. NEVER tell him to leave behind an injured comrade, or that doing so would be worth it, not even if you are said comrade; Doing so will only make him pissed at you.
Mustang and Hughes both learned this style of leadership from their commander in the Ishbalan Civil War, Colonel (later Brigadier-General) Basque Grand. A seven-foot tall Genius Bruiser, Grand led from the front, regularly risked his own neck to spare his men's lives, and did everything in his power, both militarily and diplomatically to end the war earlier. Years later, Mustang and Hughes still refer to him as "Old Man Grand" and seem quite shocked and saddened to hear of his death.
Maj. Andrei Kalinin is this to Sousuke in Full Metal Panic!, while Richard Mardukas seems to be the hardass version to everybody else, although in a twist he is particularly so toward Tessa, who is technically his superior but seems to respond to him more as a father figure.
These cases are more justified, though; Mardukas was best friends with Tessa's father, and Kalinin legally adopted Sosuke.
In Galaxy Angel, Colonel Volcott is Forte's father figure, having taken her into his care from an early age.
Miho Nishizumi in Girls und Panzer lives this trope. She was kicked off her old school's Tankery team for abandoning her tank to save some drowning team mates. At her new school, when the Tankery elective is revived, she shows in a lot of ways that she cares about every one of her team mates...and they respond by being willing to dare and do the impossible for her sake.
However he utterly fails to raise his own son, apparently, if we are to believe Hathaway's Flash. Being a career military man left him separated from his actual family for most of his life. (Though being based on the substantially altered novelization of CCA, Hathaway's Flash is semi-canonical at best.)
An antagonistic example is Vice Admiral Dozle Zabi, who actually does a badass Last Stand in order to get everyone in Solomon out to safety, from his wife and baby girl to the rookies. Quite the contrast to his ogre-like appearance.
Also from the Zekes, Rear Admiral Yuri Kellarny, who honestly and earnestly cares for his men despite being loud, obnoxious, and pissing off Ginias because he thinks it's fun. Most exemplified in episode 9 The Front Line.
Also, AEUG leader Blex Forer. He dies mid-story, though.
Suberoa Zinnerman from Gundam Unicorn is this and particularly and especially to Marida, who he was willing to launch a near-suicidal assault on the Nahael Argama whilst it was in Earth orbit for after she was captured by the EFSF.
Before his departure from the military, Zechs Merquise treats most of his men well and get incredible respect and devotion in return, but saying "fatherly" might be a stretch (especially seeing as he's only 19 years old). Lucrezia Noin probably counts a little more, seeing as she's a pilot instructor and often takes the role of the firm but caring mother figure - so much so that she becomes Team Mom (one of them, anyway) to the Gundam Pilots after a Heel–Face Turn.
Despite pulling the strings, OZ's commander Treize Khushrenada follows his subordinates rather closely and covers for them where possible (particularly Zechs and Noin), and knows the name of everyone to die under his command. When Wufei asks him how many people have died for him, Treize promptly responses that as of the previous day it was 99,822 and tells Une to give him a list of the 187 who have died in the current day's battle. He's also old enough to be a father. It's hinted he learned this from his predecessor, Chilias Catalonia.
Mwu La Flaga is a unique example of this. In Mobile Suit Gundam SEED he was the only experienced soldier and Ace Pilot above the Archangel; as such, he had a fatherly attitude toward her crew of teenagers to young adults. As Neo Roanoke in Mobile Suit Gundam SEED Destiny, he again displayed a fatherly attitude to his subordinates (one of the few Char Clones to do so), namely the Extended team under his command. Even amnesia and brainwashing couldn't take that trait away from him.
Woolf Enneacle in the second generation of Mobile Suit Gundam AGE. He's far more concerned with keeping his squad of rookie pilots alive than he is with defeating Vagan, and he takes a particular interest in Asemu... to the extent that he becomes a Parental Substitute because Asemu's actual dad is so distant. He even does a Heroic Sacrifice for him.
Alexander Anderson, of Hellsing, has a sternly parental relationship with the younger members of Iscariot (at least some of whom he actually raised in the orphanage he works at) that becomes readily apparent in later volumes. Before going into his final fight with Alucard, he orders the subordinate members of the Iscariot advance guard to go back home to the Vatican, but they disobey, staying behind to help him get to the front of Alucard's soul army at the cost of many of their own lives.
Rias Gremory in High School Dx D, who treats her Peerage like a big family in between being a strong leader. This is encapsulated in how she treats Kiba when a Heroic B.S.O.D. causes him to drop the ball in a fight: she slaps him for endangering everyone, then immediately holds his shoulders and pleads with him to tell her what's wrong like a mother worried about her son. It later turns out that deep concern for everyone under their care is characteristic of the Gremory house.
Meta Knight in the Kirby anime is this to Sword and Blade. He saved their lives, they serve him out of gratitude, and they tell people how great of a person he is and how he always looks out for them.
Yang Wen-li of Legend of Galactic Heroes embodies this trope in all but appearance (being in his early 30s and having a surprisingly delicate appearance is somewhat at odds with the classic visual perception of this archetype). Several of his own mentors, such as Alexander Bucock and Sidney Sitolet, also are examples of this trope in action (and have the wizened appearance that customarily goes with it).
Subverted in Frontier though, in that it's the Quarter's helmsman, Lt. Bobby Margot, who is the Team Dad, to the point that the Bridge Bunnies team is commonly called "Bobby's daughters". Captain Wilder, despite otherwise qualifying, prefers to distance himself from the crew somewhat (well, until Monica Lange starts actively courting him).
To become a Hokage in Naruto, one must care deeply for everyone in the village. Hiruzen Sarutobi loved everyone in his village so much, he gladly died for them. This is what makes the Uchiha Massacre even more devastating for him personally. He basically had to off the entire clan to save the village. When he saw what Orochimaru did to his men, sacrificing them to raise the previous Hokages, he cried and berated his old student, rightly claiming that Orochimaru didn't learn anything.
Neon Genesis Evangelion: Misato Katsuragi tries to be this. Her success is more than slightly undermined by her own personal issues but at least she puts the effort in... which is rather more than can be said for Gendo...
The pirate Whitebeard is like this to his men in One Piece. He explicitly refers to his crewmen as his sons, and they in turn call him "Oyaji" (which can mean father). Whitebeard is well-known to go to any length to avenge the death of any of his crew. When one of Whitebeard's crewmen is tricked into turning on him, Whitebeard's response is to call the man a fool, provide a Cooldown Hug, and tell his "foolish son" he still loves him.
While Whitebeard may be the most explicit example, Luffy's dedication to his crew and his friends is this trope in spades. He has done things for them that include but are not limited to climbing a mountain with bare hands and feet in the middle of a snowstorm, being frozen solid, and...oh, yes, declaring war on the entire world's law enforcement. And that's barely touching on how many times he's been beaten up, bitten, burned, poisoned, sliced, slashed, or otherwise put at death's door for the sake of his friends.
A very warped version of this is none other than the villainous Arlong. His only good quality is that he's as attached to his men as Luffy is to his own; because of that, he takes at least four different levels of Unstoppable Rage, each for his three defeated Elite Mooks and one when Luffy uses a fallen Mook as a shield to his bite attack.
On the Marines' side is Captain T-Bone, who is willing to tear apart his clothing to provide bandages for a train car full of injured soldiers. The extent to which he goes creeps some of the soldiers out, such as a bandage for a small bug bite. However, they are still loyal to him.
The Punk Hazard character Vice-Admiral Vergo puts up a front of this, but doesn't really care for his subordinates at all.
"Big Mom" Charlotte Linlin's men call her mama but she averts the hell out of this trope by randomly eating one of her henchmen for no reason.
Donquixote Doflamingo, one of the Seven Warlords of the Sea and, pre-Time Skip, the one about whom the least was known; one of his earliest appearances was giving a ruthless You Have Failed Me treatment to a subordinate who made the mistake of pressing Luffy's Berserk Button. But post-Time Skip, when more of his backstory is revealed (including the fact that he's The Don of a worldwide Mafia), he seems to fit this trope to a T, and it's shown that all of his closest subordinates care for him enough to die for him. Too bad the feeling isn't mutual. While Doflamingo cares about his top Officers more than his mooks, that won't stop him from ordering them to die for him. While he's clearly regretful about ordering Officers to die, it's equally clear that this is because he's losing a powerful minion, not because he's losing someone he loves. And if an officer betrays him, than they'll get no mercy. (Baby-5, the unstable Ninja Maid, seems to be an exception, due to her personality. As Law says, Doflamingo's care for someone only goes as far as how useful they are to his ambitions.
Ash Ketchum of the Pokémon anime. He takes very good care of his Pokémon and will gladly work with them to overcome any problems they may be facing. More humorously, in some more recent episodes, he'll scold them if they're misbehaving, like a father dealing with his misbehaving kids.
Tokyo Ghoul has several of these, contrasted strongly with their more Darwinian counterparts.
Yukinori Shinohara, a veteran Investigator that had retired from field work to serve as an instructor at the Academy. He returns to active duty to work with the deeply troubled Juuzou Suzuya, becoming a Parental Substitute to him. His method of leadership tends to be very nurturing, and he's shown to be a capable leader that inspires his subordinates. Under his care, Juuzou slowly grows from a feral Psychopathic Manchild into a functional human being, eventually growing into a Trickster Mentor to his own subordinates in the sequel.
Iwao Kuroiwa, another veteran Investigator, is a gruff but caring superior. This is driven home when a roomful of his subordinates have finished turning in their Wills prior to a major operation and all look terrified. He stands up behind his desk and reassures them all that he'll be there with them, immediately raising their spirits.
Yoshimura is a kind, grandfatherly figure to the staff of Anteiku and treats them like family. This inspires great loyalty in his subordinates, most of which started out as vicious criminals prior to being taken under his wing and reformed. And godhelpyou if you mess with those Yoshimura cares about.
In the sequel, Haise Sasaki's primary method of leadership seems to involve treating his subordinates like a surrogate family. He confesses that he isn't a particularly good leader when it comes to discipline and is criticized for being too lenient with them. The team even live together, with him cooking their meals and Saiko affectionately referring to him as "Maman". Nothing punches his Berserk Button like threats to his "children", and in return they are (mostly) fiercely loyal to him. Even that one exception, during a mental breakdown, has conflicting thoughts of resenting Haise and resenting that he's nothing but a burden to Haise.
Captain Gi-gang in Yona of the Dawn treats all of the crew on her ship like her kids, despite her grumpy exterior. As Yona has little memory of her own mother, the two became surprisingly close while the heroes served under her.