Detective Superintendent Yagami in Death Note comes off as something of a father figure to the other task force members, or at least Matsuda.
Tsunade toward Naruto; among other things, letting him call her "Tsunade-no-baachan" (Grandma Tsunade) instead of the formal "Hokage-sama" and letting him officially go on missions to find Sasuke (who is officially a rogue ninja with a death penalty on his head) whenever Naruto asks for it.
All the Hokages seem to have been this, even the one who was a necromancer, since he willingly sacrificed himself to save his subordinates; this goes hand in hand with their "Will of Fire" ideology. A good portion (though not all) of the Kages from the other great ninja villages seem to have embodied this trope as well.
Greed from Fullmetal Alchemist who (while he denies it fervently) is rather pleasant to and pretty protective of his underlings, making him all the more sympathetic a character. He justifies it by saying that if word gets out that he is good to his subordinates, more people will want to work for him.
Likewise, Ling gets dangerous whenever his underlings are in danger. It should really be no surprise when these two join forces... sotospeak.
En from Dorohedoro is one scary guy, but otherwise quite nice to his subordinates.
And Balalaika, both to her own gang and her outsourced labor, the crew of the Lagoon.
Nanoha Takamachi of Magical Girl Lyrical Nanoha StrikerS. She cares about her trainees. She works hard to make sure they don't overextend themselves while learning everything she can teach them. She never screams at them. She is, however, capable of blasting you into unconsciousness as a learning experience.
The most successful crews in One Piece are the ones with benevolent captains. (At least to their crews.) Monkey D. Luffy is the most obvious example of this, given that his True Companions are his very reason for living at this point, but at least one villain, Arlong, gets into this. The more recent crews exemplify this, and even the series' probable Big BadBlackbeard likes this one.
A bit of Truth in Television there. Pirate captains were supreme only while battle actually raged. They had no authority outside it, and if their crews decided to get rid of them, they were marooned. (Now there's a motive.)
Surprisingly, Doflamingo is this to members of his inner crew when he had easily dismissed and gotten rid of Disco and Bellamy once they outlived their usefulness to him. But after Vergo and Monet's defeats at the hands of the Straw Hats and Law, he solemnly thanked the former for their work and was seen to be saddened when Monet was about to blow up Punk Hazard. And later on, upon finding Baby 5 and Buffalo's heads (thanks to Law's ability), he didn't do a You Have Failed Me and even said they did the best they could.
Also Dino, to the point that he's at his strongest if his subordinates are around and he's also completely useless if they're not around. Fuuta's rankings also show that he's the #1 boss that cares about the well-being of both his subordinates and civilians.
Omega from Tekkaman Blade counts. Sure he might be trying to take over the Earth, but he actually seems to care about his troops to the point of listening to Evil explain the rivalry between him and his brother, as well as imprisoning Evil to keep him from undergoing a Deadly Upgrade. Note that Darkon, the English Dub version, is the exact opposite. HUGE SPOILER, READ AT YOUR OWN RISK. Justified. Omega's human identity is Conrad Carter/Kengo Aiba, Blade and Evil's oldest brother.
Kohta's boss in My Balls takes him out for drinks several times and one time even takes him to a brothel (the boss pays for all of it each time).
Kenzou Momoi in Servant × Service, his stuffed bunny avatar notwithstanding, speaks nicely towards his subordinates, invites them for merrymaking and leaves his desk often just to see life at work in his subordinates' shoes.
Perry's Alternate Company Equivalent, J. Jonah Jameson, is a subversion. He's a great (yet gruff) boss who protects his employees from various super-villain attacks (namely that guy who takes the great photos of Spider-Man), but hates Spidey's guts. Unfortunately, the two people are one and the same.
Depending on the Writer, most continuities make Jameson a Bad Boss, firing Peter Parker (and other employees) any time he loses his temper and only reinstating him when he must. The fact that he stands up to supervillains only makes him a brave Bad Boss.
He also anonymously pays for his employees' defense attorneys if any of them are ever charged with a crime.
In recent issues, Norman Osborn, AKA The Green Goblin, has shown remarkable concern towards his henchmen, even sincerely asking if Venom/Mac Gargan wanted out of the game.
Bruce Wayne as the head of Wayne Enterprises. In keeping with his Rich Idiot with No Day Job persona he's generally considered a bit ditzy and clumsy but generally well-meaning and likeable by his employees. He takes good care of the people who work for him, from executives like Lucius Fox all the way down to the mail boy whom he knows by name and offered a scholarship when he couldn't afford college. Probably has something do with the fact that he was ''raised'' by an employee of his family. He's considerably gruffer as Batman, though he still means well.
Mr. O'Clock, the owner of the dairy in Reid Fleming, World's Toughest Milkman, seems amazingly willing to overlook the way Reid regularly destroys milktrucks, flakes off, and generally wreaks havoc. Though Reid can be a persuasive bastard when he puts his mind to it.
Scrooge McDuck ranges from Jerk with a Heart of Gold in comics by Carl Barks and Keno Don Rosa to Jerkass in some of the Italian stories and is subject to countless jokes about how little he pays his employees — Donald and the boys frequently lament how they only get 30 cents an hour when they assist him on his treasure hunts around the globe, and his newly hired secretary says in The Life and Times of Scrooge McDuck that she spent a week's pay buying a pot of coffee for the office. Despite all this, job spots for his business empire always seem to be in pretty high demand, since he's always fully staffed and has no trouble finding employees. The thing about Scrooge is that he doesn't believe in luxuries for himself or anyone else period. So while he won't spend a cent on break rooms or heating for his employees, he presumably will pay them very well to their jobs, with the jokes about him underpaying them mainly treated as throwaway gags. One incident that stands out is from his days running the Whitehorse Bank in the Klondike, when Scrooge loaned money to prospectors to use for equipment and land claims in return for half their earnings. One loaner was a smarmy business wannabee who intended to hire workers to do all the prospecting for him, rather than do ANY work himself. Scrooge promptly changed the terms of the loan so that half of the earnings would go to him, and 45% of the rest to the workers doing the actual prospecting, leaving the lazy bum taking the loan with the crumbs.
In the Jackie Chan Adventures fic Queen Of All Oni, Jade fits this trope (at least compared to the previous bosses the Dark Hand has ended up with, like Shendu and Daolon Wong). Not only does she pay them regularly (and apparently quite a lot), she doesn't punish them NEARLY as harshly as she could for their mistakes. The Enforcers feel that she's a MUCH better boss than Shendu, and they even help her overthrow Ikazuki, since HE treated them like slaves.
Ami in Dungeon Keeper Ami, who is kind and gentle to all her minions. Of course being a Dungeon Keeper and basically a designated agent of darkness, she has tremendous trouble getting people to actually believe that.
In the Godzilla - My Little Pony: Friendship Is Magic crossover, The Bridge gives us a villainous example. The Bigger Bad, (speculated to be Bagan) gets the loyalty of numerous evil kaiju not only by a show of force, but by offering and giving them exactly what they wanted most. Most pledged their loyalty without hesitation
The My Little Pony: Friendship Is Magic fanfic Address Unknown has Post Haste, Derpy's boss at the Ponyville Post Office. After she's put on probation by the Cloudsdale office and then almost immediately fired - over an accident that was actually Twilight's fault - Post wastes no time in offering her a job, expressing his disgust at her previous boss's actions (the aforementioned firing, along with the pleasure he took in filling Post in on her "miserable failings") and makes it clear that he has a considerably greater tolerance for mistakes.
The The Legend of Spyro fanfic The Legend of Spyro: A New Dawn depicts Big Bad Deadlock as this. She in fact overthrew the Naga's previous queen and took over herself because said queen was an abusive tyrant; she treats her minions well and makes sure everyone is paid for their services, and some of the Naga even admit that she's the best queen they've ever had.
In the Pokemon fanfic Natural Liberated, Clemont is depicted this way. He treats all members of the Net, no matter how new they are, with equal respect and listens to everyone's ideas. This happens despite the fact that all of the members are older than him.
El Guapo from ¡Three Amigos! is a villainous example of this trope, shown receiving a sweater from this henchmen for his birthday and wearing it for the remainder of the film. He even treats his birthday celebration like a party for everyone.
Joe in Empire Records. He's basically a father figure to all his young employees, and a legal foster father to one of them.
Gru in Despicable Me. He may experiment on his minions occasionally, but he treats them well and cares for them, even kissing all of them goodnight.And he knows all their names! In return, the minions all love and adore him.
He also has no issue with them throwing wild parties in their off time as long as he can grab the ones he needs. Even though said wild parties are in his basement.
He also sends two minions up a pole to safety before himself, despite that meaning there will be no room for him to escape the monsters too.
In the Richie Rich movie, Richie's dad is a firm believer in not firing employees, claiming that job security makes better and happier workers. The one exception he eventually makes is the Big Bad.
George Newman in UHF instantly becomes one the moment he steps in as manager of channel U62. Despite his brief depressed moment when the station seems to be going nowhere, he snaps right back to his cheerful Crazy Awesome self the moment StanleySpadowski becomes a hit with his show. His willingness to put anyone on the air doing anything brings a contagious energy that quickly spreads to the entire station and makes them the highest rated channel in town.
Independence Day: Marty (Harvey Fierstein) - Jeff Goldblum's Camp Gay boss at the satellite TV company. His immediate reaction on hearing of the potential danger of the UF Os is to tell everyone to stop work and get to safety in the basement NOW. This is a media company that is covering the event: shutting off transmission long before others even guess of any danger would cost them $millions.
G. W McLintock, the titular hero in the John Wayne Western comedy McLintock!, is very much this trope. After he hires Devlin, he recognizes how the young man had to swallow his pride to beg for a job, and assures him, "I don't give jobs, I hire men," and if Devlin will put in a fair day's work, "For that I'll pay you a fair day's wages. You don't give me anything, I don't give you anything, we both hold our heads up." Seeing that Devlin's family are in dire financial straits, he then gives his friend Drago some money to give to Devlin, saying, "Tell him I pay my men a month in advance." Throughout the movie, he treats his employees fairly and is friendly to them, especially Devlin whom he learns to respect as a fine young man and hard worker; when Devlin and McLintock's daughter Becky announce their engagement toward the end of the movie, he's overjoyed.
Mr. MacMillan from Big. He will listen to honest criticism and complaints about his toys and when a good idea is brought forth, he will go with it. He also does chop sticks for fun.
In The Thrawn Trilogy, Grand Admiral Thrawn was far too remote from his troops to really qualify as a father figure. His image was of an alien genius, strange but far too skilled to be brushed aside. But he wasn't unnecessarily cruel to the people on his side, he rewarded quick thinking, his Commander Contrarian pretty much adored him, and Thrawn was respected and trusted. Thrawn used a small measure of fear, certainly: the Grand Admiral realized that fear of failure was a powerful motivating force in a military the size of the Empire. But Thrawn's ability to invoke a sense of pride in his troops was his most powerful asset. Palpatine inspired arrogance and callousness in his officers; Thrawn made his men proud to be Imperial soldiers. Thrawn's officers would have willingly died for the Grand Admiral.
Repeatedly, some of his crewers are incapacitated by Joruus C'baoth. Thrawn always has more bridge staff take them to sickbay. Sure, it's the pragmatic thing to do; they're not dead, just useless for a while. But you never have Daala or Krennel or any other Imperial who doesn't switch sides saying this. If they give any orders about a fallen crewer, it's "Clean this up".
This goes into Moment Of Awesome territory when he promotes a subordinate who failed to capture Luke Skywalker, but both admitted his failure and showed innovative thinking. Thrawn's XO Pellaeon notes immediately afterward that the crew of the Chimera had respected Thrawn before, but now they'd die for him.
A classic example is Fezziwig in A Christmas Carol — the good-natured employer of Ebenezer Scrooge in his youth. This memory becomes the first step in Scrooge's path to become a better man.
He has the power to render us happy or unhappy; to make our service light or burdensome; a pleasure or a toil. Say that his power lies in words and looks; in things so slight and insignificant that it is impossible to add and count 'em up: what then? The happiness he gives, is quite as great as if it cost a fortune.
Scrooge himself becomes this to Bob Cratchit in the end.
The captain in the Phule's Company novels. He not only throws large quantities of money into shaping up the Omega Mob, but devotes much time and thought to figuring out their needs and meeting them, even to the point of ignoring his own.
From the Harry Potter series is Albus Dumbledore, headmaster of Hogwarts School of Witchcraft and Wizardry, firm believer in second chances. He will defend his staff members to anyone, even the Ministry of Magic if need be, and don't you dare try to eject anybody from the school building while he's in charge.
Also, when Dobby (A Non-Human Sidekick of sorts) comes to work at Hogwarts and asks for both holidays and paid work (something that has never happened before), he agrees straight away and offers more then a considerable fair wage.
He actually offers him so much, Dobby demands lower pay and fewer days off!
Commander Vimes is repeatedly proven to be a much better boss than his attitude suggests. Although he doesn't like anyone much, his men are willing to put up with his roughness because they know that when the chips are down, he's got their back; in fact, after most of them leave during Fred Colon's time as Acting Captain, the only way Carrot can convince them to come back is by telling them he and Commander Vimes are back.
One of the reasons many of the Guard left during Fred Colon's tenure was because he made racist comments while members of said races where standing feet away from him. When it's pointed out to them that Vimes makes similar comments all the time, they say that they don't mind when Vimes does it, for the reason mentioned above.
As far as Sam Vimes is concerned, the race of any Watchman is Watchman.
The men of his camps never had known him to be in a hurry or to lose his temper. Discipline was inflexible, but the Boss was always kind.
Dirk Struan from Tai-Pan is a self-made man who started out as a cabin boy under a tyrannical captain. When he becomes a ship owner, he pays wages on the day, in silver, and equips his ships with the best of everything. Sailors fight for the chance to work aboard one of his ships.
Hank Rearden and Dagny Taggart of Atlas Shrugged treat their employees with the utmost respect and consideration. Dagny is quick to thank and promote employees like Owen Kellogg who distinguish themselves well with their ability and effort, and Rearden pays higher wages than any union would ever demand... in exchange for the most talented, competent, capable work force money can buy.
The Count of Monte Cristo is this (although he combines this trope with quite a bit of Fair for Its Day), as was his master, Monsieur Morrel. When Edmond was framed for Bonapartist collaboration and imprisoned in the hellish Chateau D'If, Morrel was the only person who tried to save him, though it was extremely politically dangerous to do so. Edmond rewards this compassion with Undying Loyalty to Morrel's family, and this is the source of many heartwarming moments throughout the book.
With a twist in a story by Heinrich Böll about the (fictional) poet Bodo Bengelmann. After finishing school, his practical parents insisted that he started an apprenticeship. Which he did, in a shop for wallpapers. As the author comments, the job was an ideal environment for him: The shop owner, his boss, was most of the time so drunk he passed out, and Bodo wrote poems on the back of wallpapers. - Then he used his first wage to send copies of his poems to all newspapers and magazines, and since a good part of them answered, he became rich and famous.
Lord Dreadgrave the Necromancer in Mogworld got an unpleasant surprise when the horde of zombies he raised turned out to be freewilled, but rolled with it (partially to avoid being ripped apart by said horde, admittedly, but he follows through on the promises he made). Jim appreciatively mentions how he acts on their ideas, remembers their names, and gives them props when gloating to adventurers.
Live Action TV
Just about every serial crime drama and occupational drama on English-speaking television, such as Law & Order, CSI: Crime Scene Investigation, ER, etc. Even the designated-asshole superior officer turns out to have a heart of gold by the series' end.
Capt. Donald Cragen of Law & Order: Special Victims Unit is portrayed as a somewhat stern but understanding father figure who gives the detectives a great deal of leniency because he trusts their ability to get results.
Conrad Ecklie in CSI: Crime Scene Investigation grew into the role over time. When he first got promoted to Assistant Director in season 5, he had a very rocky relationship with Grissom and his crew (especially Grissom), which eventually led to Ecklie splitting the team up. It begins to change in the season 5 finale, when Nick gets kidnapped and buried underground, as he becomes vital to the investigation and eventual rescue. Since then his relationship with the crew has become more cordial and he's given them far more leeway than he used to.
Sometimes Mac seems to think of his team as family of sorts on CSI NY-he did tell Christine the job had become his world. It's obvious how close he is to them all. He is no-nonsense on the job but makes up for it.
Jed Bartlet, The West Wing. He openly describes the senior staff as family, and there are many instances where one of them offers to resign for some screw-up, but he never accepts. The only time he does fire someone is Toby in Season 7 for the national security leak.
Leo McGarry as well, excepting Season 5. Particularly his kind treatment of the woman who leaked his drug rehab records to House Republicans, and of Ainsley Hayes when the other staffers were still being hostile towards her:
Leo: Kid, the others are going to come around. See you've got to remember that the people you're talking about live their lives under seige, 24 hours, every day. At a time when they're trying with all their might to do good, you're in their foxhole. [...] I'm a recovering alcoholic — bam! Radio, TV, magazines, cameras in front of my house, people shouting at my daughter at the ball game. Editorials, op-eds, "He's a drunk, he's dangerous, he should resign."
Ainsley: I wrote one of those op-ed pieces.
Leo: I know.
Walter Skinner in The X-Files, although his benevolence is most certainly confined to his actions, not his demeanor.
A villainous example is "The Clairvoyant", a.k.a. John Garrett, who is surprisingly friendly towards those who work for him (even though he was much less friendly before he was exposed as a member of HYDRA) and likes to see them enjoy their work.
Rear Admiral A.J. Chegwidden and his successor Major General Gordon Cresswell in JAG.
Also their boss, Secretary of the Navy Edward Sheffield.
In a somewhat uncommon villainous example, the three Gaiark Pollution Ministers from Engine Sentai Go-onger are this, most evident in Yogostein. They often praise their Monsters of the Week for doing well, even if they still didn't beat the good guys.
Jack Donaghy, from 30 Rock cares about main character Liz Lemon and obsesses over staying a hero figure to NBC page Kenneth Parcell.
Jimmy James too. He loves to mess with his underlings, but in the end is always looking out for them.
David Brent and Michael Scott from the British and U.S. versions (respectively) of The Officethink they're being benevolent, but are so bad at it they wind up being the Stupid Boss instead. Michael comes closest, even having moments where he actually is helpful. (Supporting Pam after her failed art gallery show, for instance.)
David on the other hand gets extremely angry and defensive when his "advice" is rejected or disputed.
Col. Henry Blake and, even moreso, Colonel Potter on M*A*S*H.
Adelle DeWitt from Dollhouse is an odd example — her general persona is of an Ice Queen, a tough, non-nonsense businesswoman, and in her particular line of work she is even willing to kill if necessary... but she also cares about her employees, and they know it. (Which is what makes her giving Topher's schematics to Handling in Season Two a rather shocking Moral Event Horizon.)
Sam Merlotte from True Blood is a good boss, a great friend, and a kickass shapeshifter.
Siegfried Farnon from All Creatures Great and Small is a kindhearted guy underneath his brashness. The time when he defends Herriot's decision to put down an expensive, and mortally ill, horse for his first case bears that out.
Paul Lewiston of Boston Legal may be the frustrated Only Sane Man in a firm made up of gun-toting, sex-addicted, filibustering, cross-dressing, midget-fetishising Bunny Ears Lawyers, but he still manages to put up with them all. And from season 2 onwards, after reconciling with his daughter and meeting his granddaughter, he becomes much more relaxed and pleasant.
Alan Shore, one of the aforementioned sex-addicted, filibustering, cross-dressing, midget-fetishising Bunny Ears Lawyers, is good to work for too. Every assistant or secretary he's had went away better for having been hired.
Arthur Carlson in WKRP in Cincinnati isn't an effective boss, but he's well-meaning and treats his employees with respect. Even Herb.
Rube in Dead Like Me is a Jerk with a Heart of Gold who keeps his Rag Tag Bunch Of Misfits running about as tight a ship as can be reasonably expected. He often shows his softer side with George, and once carried Mason to his place to let him sleep off a drug overdosenote Since reapers have a Healing Factor, overdosing isn't such a big deal. Basically, his subordinates love and fear him at the same time.
Mayor Richard Wilkins from Buffy the Vampire Slayer is a swell guy to work for. He's always got a kind word, he asks after your family, he encourages good dental hygiene and good nutrition, and he discourages swearing and encourages teamwork and esprit de corps. He'll even pay for a new wardrobe and an apartment if you happen to be a homeless psychotic slayer in need of an outlet for your violent tendencies! Oh, and he wants to transform into a giant snake demon and eat everyone in the city. But what boss is perfect, right?
Cam Saroyan on Bones, pretty much. She's professional at work, but is still pretty enganged with the lab team at the same time. Goodman wasn't *too* bad, but he was more stern than Cam.
Art Mullen on Justified is good boss and friend. And considering all that Raylan's put the Lexington office through, should probably considered for sainthood.
Deconstructed by Max in the 2 Broke Girls episode "And the New Boss." She's not comfortable hiring an intern to work for them for free, nor with firing said intern when she starts taking advantage of Max, despite Caroline's repeated entreaties to do so. Only when she finds that Ruth (the intern) referred to her as "the dumb one" in a text does she finally do it.
Admiral Malkor in Power Rangers Megaforce. Yes, he's the Big Bad and not exactly nice, but unlike previous villains, he treats his subordinates with true respect and as equals. In fact, the worst thing he does towards them is scold them if they fail him too many times or if they fall before their enemies in battle.
While Angel was usually a pretty bad boss in the fifth season, openly despising and occasionally executing employees, he does have a moment of this towards his ditzy vampiric assistant Harmony. After unexpectedly being a pretty good assistant most of the season, she betrays him to his enemies. When he confronts her about this, reveals he saw it coming, and fires her, she asks him for a recommendation. He not only says yes, but when she brings up that he might well not survive he reveals that it's in her desk. Meaning that at some point he realized that Harmony was going to betray them and leave him to die, and he responded by taking time out of planning his assault against the forces of evil to sit down and write her a letter of recommendation. That's class.
Batman: Arkham City: While not necessarily a very good boss, Two-Face seems to be the only villain who cares about his underlings, giving inspiring speeches and trying to raise morale among his minions.
The old dean of Evil Academy was so good, in fact, that the evil reputation was used as a defense mechanism to keep idiot heroes out. The one hero it should have kept out, however, was far more worthy of this forged reputation.
Champloo: Hyahyahya! That whole tale of a vicious Overlord was an urban legend we passed around to protect the Netherworld from stupid heroes. A bright red lie, redder than the ripest tomato! He simply wanted a peaceful Netherworld, a place where demons could live a carefree life. He was indeed the strongest Overlord...but at the same time, he was also the greatest Demon King!
Would you believe Geese Howard is like this? His Dragon, Billy Kane, is treated like a friend more than an employee, and he even treats his minions to drinks on occasion.
In Jak and Daxter, Osmo is to Daxter what Samos is to Jak, in a way: he compliments and praises Daxter for his excellent work.
The Illusive Man of Mass Effect is an Affably Evil boss who is genuinely supportive and helpful towards his subordinates in every way possible and is never anything less than completely supportive and trusting of Shepard's actions and decisions (until a certain one comes up, however). Hell, he calls Shepard just before Shepard launches what is by all accounts going to be a suicide mission to offer moral support and show concern for Shepard's safety. Just don't betray him. Bad idea. However by the third game he has Jumped Off The Slippery Slope and any compunctions he may have had are now gone in place of mass-indoctrination and "Contract Terminations" of scientists after they're finished with their assignments.
Shepard him/herself can be played as a Benevolent Boss. S/he can look out for each newly recruited team member, and can make side trips that help each member with what are really personal issues. When people are kidnapped by the minions of the Big Bad, Shepard is able tomake a suicide run to try and save them.And if you're a good enough boss, you can save most of the kidnapees and your entire assault team. Of course, Shepard could also be played as a colossal dickosaurus.
Admiral Hackett from the first game also counts. He compliments Shepard upon successful completion of certain side missions, and in the second game, it's revealed he's the sole reason the Alliance isn't trying to arrest and interrogate you.
Bowser of Super Mario Bros. is this in the RPGs. He's generally beloved by his troops who follow him out of admiration rather than fear, has a True Companions-like bond with them and in Super Mario RPG is actually incredibly forgiving of them (letting two of his minions live in the Monster Town where they're truly happy rather than forcing them back into his service). That is of course, barring his quick temper.
In the end of Mario & Luigi: Bowser's Inside Story, Bowser lets Private Goomp, Sergeant Guy and Colonel Paraplonk stay even after they betrayed him for Fawful (they were brainwashed), whereas Kamek wanted to kick them out of the castle.
Yuri from Infinite Space. Bastian even notes this is the reason why he is a better captain than his rival, since Yuri forms a bond with his crews rather than simply treating them as the power to run his ship. In terms of gameplay, choosing the "benevolent" options will usually give pretty nice stat bonuses.
Inspector Chelmey, the Inspector LestradeExpy from the Professor Layton series, reveals himself to be this in the third game. He admits to Layton that his right-hand officer, Constable Barton, makes a metric ton of mistakes and probably should have been fired — but Chelmey will not allow him to be, because Barton tries hard and means well and Chelmey trusts and is fond of him.
Byakuren Hijiri, Satori Komeiji, and Eiki Shiki are this trope in Touhou. Other masters? Not so much.
Metal Gear's Big Boss arguably qualifies for Outer Heaven and Zanzibar Land, as many of the soldiers seem to praise him.
Indeed. His army in Metal Gear Solid: Peace Walker is consisted of defeated soldiers and volunteers, and he never gave them much trouble (The worst thing he did is fired them, usually if Mother Base is overcrowded), and in Metal Gear 2, he even helps and recruits his former enemies. You can't get a mercenary who is more benevolent than that.
In Final Fantasy VI, General Leo qualifies for this trope, though he is not a boss in the video game sense. When he is first seen by the party he shows his benevolent nature by refusing to let his soldiers charge recklessly at the enemy, determined to minimize casualties on both sides. He later shows modesty when he tells Terra he is no better than Kefka (the main villain in the game) because he allowed him to get away with his crimes. He is killed by Kefka during his short time being controlled by the player.
Yamato from Devil Survivor 2 is an interesting play of this trope. He is a Jerk Ass who calls his subordinates "trashes" and he treats his subordinates like tools. On the other hand, he is a fair boss. He treats those who can do their jobs well nicely and he doesn't chew or punish employees that fail to do their jobs, but simply reassigns them to less demanding tasks. He doesn't throw his subordinates' lives needlessly and he doesn't ask them to do anything he doesn't or can't do himself. No wonder why the J Ps respect him and are loyal to him.
Zepheniah Mann from Team Fortress 2 hated his family (he didn't give a damn when his wife died giving birth and he loathed his sons) but he seemed to be fond of his employees. In his will he gave his maid Elizabeth his personal estate and his tracker Barnabus Hale his business empire. He gave his sons a worthless piece of land to fight over.
In Dragon Age II, Hawke can be played this was. They can double the wages of the Ferelden workers in the Bone Pit, as well as protecting the workers from dangerous creatures that threaten the mine. Hawke lets Bodahn and Sandal stay at the Estate, despite insisting that Bodahn doesn't owe them for saving Sandal's life in the Deep Roads. They can also free Orana from slavery and offer her paid work as a maid. The Codex later mentions Hawke encouraged her musical talents and paid for her lessons out of their own pocket.
Kil'Jaeden in World of Warcraft is this, especially when compared to his co-dragon Archimonde, who is the definition of a Bad Boss. While Archimonde in most cases would instantly kill an underling who failed a mission, Kil'Jaeden is more than willing to give second chances, especially if it's not the underling's fault, and will only exterminate the poor mook if he is a complete failure. That's pretty damn decent for someone who is the temporarily replacement for the whole franchise's currently missing Big Bad, and thus one of the most powerful and evil beings in the universe, barring Sargeras himself and the Old Gods.
Mr. House in Fallout: New Vegas. He's arrogant, sure, but he pretty much treats the Courier with exactly as much respect as he is shown in turn, is open and honest about his plans, trusts his employee to make his/her own tactical decisions, and provides him/her with full access to a refurbished luxury hotel suite and cocktail lounge.
David Sarif in Deus Ex: Human Revolution. He's not perfect: he's guilty of augmenting an employee above and beyond what's needed to save him via a loophole in the employee's contract, stalling the local police to send said employee to deal with a hostage situation to prevent a prototype military aug from being exposed, and installing a backdoor into his company's network so he could secretly investigate the same employee's background. In all other respects he's an Honest Corporate Executive who treats his employees like family who ultimately cares less about money and more about making augmentation more widespread. Even those shady moments could be considered examples of his benevolence. Sarif has such an idealistic view of augmentation that he may have honestly considered augmenting Jensen to such an extent to be a favor. Sarif spared no expense in doing so too since all of Jensen's augments are top of the line goods. Sending Jensen in to the hostage situation ahead of the police was also something David did for the sake of the company since he's got more faith in Jensen, a capable badass who has augmented to be even more badass than he does in the police. As for the backdoor into his network, David arranged that because he wanted to make absolutely sure that Adam wouldn't be a liability given the fiasco that resulted in him leaving SWAT. If Adam points out to David that the backdoor made the disastrous attack on Sarif Industries possible in the first place during the Social Confrontation, David will likely acknowledge that he endangered the company and its employees and apologize.
Much of In Your Arms Tonight takes place in and around the protagonist's workplace at an interior design firm, where she has not one but two benevolent bosses:
Kippei Ebihara, the manager of the design department, is strict and demanding of his employees but also fair; he's a hands-on manager who does a lot of field work himself rather than leading from a desk and is very supportive of employees who prove their work ethic and willingness to improve.
Above Ebihara is Hana Ichikawa, the CEO of the company, who has a friendly relationship with the protagonist and is the person responsible for promoting her into the design division. She is understanding and tolerant of the foibles of her employees and acts as a bit of a Trickster Mentor at times.
Hiroshi Kirisawa, the head of the 2nd Unit in Metro PD: Close to You, encourages his subordinates to run their investigations however they see fit, and he's always there to back them up should they run into trouble or need his support in any way.
Lord Doom, an Evil Overlord active in the Global Guardians PBEM Universe. His henchmen and operatives are well-paid and enjoy excellent benefits (including total-coverage health insurance, college tuition assistance, low-interest housing loans, a retirement plan, and a generous life-insurance policy. They also know that if they are ever arrested, all they need do is keep their mouths shut and Doom will use his vast resources to get them the best legal help in the world. Of course, if they do talk to the cops, things go very different.
Skitter from Worm listens to the problems of her minions and takes steps to resolve them, doesn't ask them to do anything immoral that they aren't comfortable with, and does her best to keep them safe from other supervillains.
Donnie DuPre from Demo Reel is probably too much of a Wide-Eyed Idealist to be actually effective as a boss, but he thinks the others (including the terrorists) are his best friends within five minutes of meeting them, and tries his best to keep everyone's hopes up.
Given she only employs three of her own friends, perhaps not so surprising. Marten's bosses have a tendency towards this trope though (among others).
Punch an' Pie plays with this trope in the parallel story arcs regarding Angela's boss George and Heather's boss Brian. George is a Jerkass that nobody in the store likes, while Brian is a cheerful and upbeat guy who is naturally likable. Both of them end up in compromising sexual situations with their employees. George decides to Take a Third Option and Pet the Dog, resolving his conflict to the benefit of all; Brian, on the other hand, turns bureaucratic (albeit with a helping of regret) when confronted with conflict.
Then there's Angela's beloved former boss Dawna, pretty much a paragon of motherliness and benevolence.
Mike Bookseller has Fab, who is smart, reasonable, and well-liked by his employees.
Subnormality makes the claim that this is the worst boss you can possibly have; despite all the varied and sundry overtly horrible bosses for whom you could be working, this one makes you feel good about your terrible soul-crushing job.
In Wapsi Square, Monica's boss, despite his slight ineptitude at times, genuinely cares about the museum employees, and even set Monica up with her boyfriend Kevin. In addition, Heather's boss once told her that she had spent too much time working, and that she needed to go out and have fun (yes it was a direct order).
Tina the demonic barrista is this to her assistant. Whether she's the owner of the coffee shop or an employee herself is still nebulous.
Zig Zag, founder of the porn studio "Double Z Studios" from the webcomic Sabrina Onlinedefinitely qualifies; her employees totally adore her (with the exception of Darke Katt, though she always was a bitch to start with), she treats her male porn stars like people rather then pieces of meat, and she insists that she be addressed as Zig Zag, not 'boss' or 'ma'am' to keep her connection with her workers as close as a family.
Hank Scorpio: Great boss, just happened to be running a criminal empire. He even went so far as to give Homer the Denver Broncos as a going away present. (Homer had really wanted to own the Dallas Cowboys, but while Scorpio couldn't get them, he was the only one who ever told him that his dream to own them wasn't crazy.)
Smithers once attempted to become this after briefly being placed as Burns' temporary replacement after Burns was arrested for a theft of paintings, but after Homer, Lenny and Carl started mocking him behind his back about his allowing them to essentially goof off... well, you get the picture.
Homer himself played it quite straight when he became CEO and overthrew Mr. Burns, until he realized that he was missing out on his family and gave up the position. (Burns has a seemingly heartfelt conversation with Homer about the time running the plant costs someone, only to hit him with a tranq dart and attempt to wall him up in a mausoleum. Being as frail as he is, he's barely finished a row of bricks by the time Homer wakes up. The bemused Homer puts a blanket on Burns's shoulders and walks off while Burns continues to add bricks.)
A better example is when Homer is put in charge of the Nuclear plant out source in India. Mostly we see his megalomaniac behavior after a few silly comments and a fortune cookie, but it turns out in the end that the worshipful behavior from the employees is due to him giving them all the benefits typical to American workers, but denied outsourced labor, such as unions, vacation time and severance pay, to Burns's dismay. Their chanting while cheering him on translates to union slogans
J. Gander Hooter from Darkwing Duck: Absent-minded, a bit on the eccentric side, but an effective and fair mission control to Darkwing and the agents of S.H.U.S.H., generous with praise and sternly serious about getting results on protecting the world from F.O.W.L.
Rebecca Cunningham from TaleSpin usually leans towards this, generally treating her employees more as friends and has yet to fire one despite their numerous acts of stupidity. That said, due to having slight Control Freak tendencies and a bit of an erratic personality, she can have shades of a Mean Boss or Pointy-Haired Boss at times (especially in early episodes).
Iroh from Avatar: The Last Airbender is a good candidate for this trope. He withdrew his troops from a two year long seige of Ba Sing Se when he realized that it was pretty much hopeless (granted, it took the death of his only son to see this....), and he acts more or less like the voice of reason to the troops under Zuko's command during his exile. It is probably safe to say that Iroh is the only reason that the crew did not mutiny the entire time they were under Zuko's command.
Zuko has his moments in the first season too, despite being a Jerk Ass at the same time. He nearly kills himself saving the life of his ship's helmsman, and this is after his crew spent a good half of the episode bad-mouthing Zuko for his jerk assery.
Breakdown of Transformers Prime is a villainous example. He's an antagonist, but he tells his subordinates to keep up the good work and that he understands the job the Vehicons were doing can be thankless. Considering Decepticon M.O. is usually that the best you can hope for is barked orders and that your superiors only threaten you for incompetence, that's a step up.
Gravity Falls: Mabel starts out this way when she gets to run the Shack in "Boss Mabel". It doesn't work out after she becomes overly generous with her employees.
Although jokes about Scrooge McDuck's underpaid employees are just as widespread in DuckTales as in the comics, no one can deny that Scrooge's employees all like working for him. Launchpad once accepts a job from Flintheart Glomgold, only to get fired after a few minutes for crashing the plane; Launchpad muses how Mr. McD "never fired him that fast" and is eager to go back to presumably the one boss in the world patient enough and tough enough to hire such a pilot. When the boys accidentally get Scrooge's butler Duckworth fired, they apologize and tell him they'll miss him but still think any job "is better than being Uncle Scrooge's slave"; Duckworth says indignantly, "I love serving Mr. McDuck!" And when Scrooge goes looking for three cargo ships of his that have disappeared, he finds his crews being held prisoner (along with many others) on a bizarre seaweed island. Scrooge's captain tells him how hearing that he had arrived made them all feel hope for the first time in years, and they all had faith that, with him leading the way, they could escape (Scrooge doesn't let them down). Employees of McDuck Enterprises all seem to consider their boss benevolent, even if Good Is Not Nice.
French explorer Jacques Cartier was an accomplished seaman, never losing a ship or a man on his voyages. As a result, he was very popular, and men were often eager to join his crew.