In Final Fantasy XIV, Gaius van Baelsar. He acts as a Parental Substitute/Team Dad for two of his generals, promotes based on achievements and merit rather than social status and is visibly upset when he learns the heroes killed one of them.
Also, said general, Rhitahtyn sas Arvina. He is initially flanked by two Imperial mooks when you confront him, but he sends them away when he realises they would just get killed if they tried to help him.
Big Boss in the series in general. The kids at Zanzibar Land called him their "One-Eyed Uncle", and there is a very good reason why his men are genuinely loyal to him instead of serving him out of fear.
He's also something of a deconstruction. When things go wrong and his soldiers die, Big Boss really has a tough time dealing with it. Eventually he can't take it anymore and thingsdon'tendwell. Notably, during the destruction of Mother Base, he's completely calm for almost the entire fight, until he sees a good number of his men cut down in front of him, at which point he goes into a rage and almost needs to be dragged back to the chopper.
And later on in the game, he comes back, as an Ubergestalt. At first he appears to have done a Face–Heel Turn, but defeating a particular boss later brings him back to his senses and memories, and returns to the Red Sprite with final words of encouragement for the Strike Team. Depending on your Character Alignment, he'll either decide you'reunworthy of your existence, or assist you in destroying the Schwarzwelt and saving humanity.
Although the Kirby series isn't exactly known for its deep characterization, what we see of Meta Knight's interactions with his endless army of Faceless Goons seems to indicate he plays this role for them; yet another one of the reasons he's the resident Worthy Opponent and Hero Antagonist. Kirby Super Star's "Revenge of Meta Knight" makes it a bit more explicit. He tells his crew to abandon ship before it crashes into the ocean while he distracts Kirby with a final duel. His crew likes him too much and they decide to fight Kirby first. He snaps at them for being so willing to throw away their lives, then apologizes under his breath for allowing things to get to the point that they would have to.
Captain Brenner/O'Brian in Advance Wars: Days of Ruin, who indeed serves as an idealized counterbalance to the leader of the other Rubinelle/Laurentinian faction.
Lt. Colonel Daitetsu (from Super Robot Wars) actually mentions that he feels this way to his second in command, Tetsuya.
Master Big Star from Disgaea 3 fills this role nicely. The late King Kricheveskoy also appears to have been one, if Etna's accounts are anything to go by.
King Kricheveskoy definitely fits in Disgaea. The vassals scattered around the castle make many mentions of it: when a former enemy of the late king's shows up and attacks Laharl, they go to his defense explicitly in honor of Kricheveskoy's legacy. Later, after Laharl becomes the new Overlord, one of them even says he cannot think of anyone but Kricheveskoy as truly being the Overlord. None of them ever have anything but kind words for him, and they mention him often.
Valvatorez of Disgaea 4 may be strict with his Prinnies, per his job as a Prinny Instructor in Hades, but he treats them with respect and is willing to issue sardines for exceptional performance, even if it means breaking up a culling. As a result, his Prinnies are exceedingly loyal and decently competent.
The yellow Prinnies of Toto Bunny are charged with assisting the Overlord in helping keep the peace, and are duly respected by the royal family. Their loyalty and competence is equal to that of Valvatorez' Prinnies, to the point one such Prinny steals a plate of curry from Seraphina's pocket Netherworld, annihilates several of Seraphina's Prinnies and endures beatings from the rebel army and the Lost just to aid her young master and thinks nothing of it.
Ace Combat Zero also featured a female version, though in a minor unnamed and unseen character. In one mission you are ordered to destroy a Belkan base with a female commander who can be briefly heard through radio transmissions. Upon other transmissions from the soldiers in the base, it can be heard that they greatly admire her, for her beauty as well as her courage, and all see themselves as equivalent to her sons. At the end despite a brutal defeat she even reassures her troops and says they all fought well and with honor.
Selvaria Bles is arguably a female version of this trope according to the DLC. Taking the front lines alongside her soldiers, giving up her cot for exhausted subordinates, rewarding her troops for going above and beyond their normal duties
Hell, there are hints of this even in the main story. More often than not, she'll issue the order "All Units Heal".
Takeda Shingen from Sengoku Basara cares deeply about his men, and in particular has a fatherly affection for his young ward Yukimura.
Chosokabe Motochika is also a good example, though he's rather young so his crew see him as more of an older brother than a father.
Tachibana Muneshige and Maeda Toshiie also claim that their soldiers are like family to them.
One can't discuss Sengoku Basara without also mentioning Date Masamune, who doesn't give a second thought to waltzing into a trap while badly wounded to save a handful of his subordinates.
Despite his ruthless demeanor, Toyotomi Hideyoshi cares a lot for his subordinates, which is why they're so fiercely loyal to him, especially Hanbe and Mitsunari. It's Hideyoshi's care for his men that makes him oppose Nobunaga in SB2.
Shi-Long Lang, the Interpol agent from Ace Attorney Investigations is intensely devoted to his men and is adored by them in return. This is both played for laughs (as when he insists that the 99 agents under his command should not count off from 1 to 99, but should all count off as '1' because they're all #1), and played totally straight when he takes a bullet for one of his agents, even though she had been revealed as a spy in his unit and a wanted murderer not five minutes prior, on the grounds that she was still one of his agents, and therefore it was his responsibility to keep her from harm.
There's a scene earlier than the above spoilered one that highlights just what extremes Lang takes this trope: He gives one of his men a birthday present. But it's not for the man he gave it to; It's for the man's younger brother's wife's younger brother.
Yuri Cosmos, from Dual Destinies. He may care a bit too much about himself, but he definitely cares about his men, and will and has done anything in his power to save them during the space center bombings.
The Total War games often have 'Uncle to his men' as a trait for Generals—it generally results in increased morale, though higher levels of the trait introduce penalties to discipline, reflected in shorter strategic-level marching distance. 'Social Drinker' also qualifies, as the description involves him having a flagon or two with his men.
Commander Shepard can clearly be this in both games if played as a Paragon; striking up friendships with all his/her subordinates and often passing along compliments, encouragements, and risking his/her and the party members' lives to rescue them in the sequel, as well as fulfilling the "cut up about losing a squadmate" portion of the trope quite handily in the first game... Not to mention, arguably the most dangerous thing a person can do, is attempting to harm the people under his/her command, current or former. Some variants of Renegade Shepard could also qualify as a Jerk with a Heart of Gold version of this.
Captain Anderson is also this, especially towards Shepard. Mass Effect 3 reinforces this in particular with Anderson's last words to her/him.
Anderson: You did good, [child/son]. You did good. I'm proud of you.
General Victus from Mass Effect 3 is shown to have this dynamic with his men. One of the reasons he's reluctant to accept his promotion to Primarch is that he'll have to leave his men on the battlefield while he goes politicking. Even when convinced, he requests a few minutes to say goodbye to his subordinates.
In Sabres Of Infinity Should you take the time to gain your men's trust and respect, you yourself can be this.
Sergeant Lanzerel: Begging your pardon sir, but we missed you. It'd be a fine honour to serve under your command again.
Samurai Warriors 2 plays with this for magnificent, Crazy Awesome and funny effect: Nene is a mother to her men - in that she warns them to be careful with their knees and elbows, tells the enemy to stop firing cannons so as not to wake the neighbors (and upon beating them, remarks: "Such weak enemies! Who's feeding them anyway?" with some concern on her face), and, in general, seems to be blissfully unaware of how a battle between two armies is supposed to work - made all the funnier by the fact that she's a very skilled warrior, and that the morale of the men who hear her motherly warnings increases.
In a slightly more traditional bent, Ujiyasu Hojo from 3 treats even the Mookiest of his soldiers like his own kin, taking the time to speak to them personally and address their worries, a bit like a rough old uncle or grandfather. Thanks to this treatment, his men are absolutely fanatical in their loyalty to him as a result.
Surprisingly, General Donald Morden from Metal Slug was said to have been this back when he was a Vice Admiral in the Regular Army. When he eventually resigned due to his son's preventable death, everyone formerly under his command followed him out, sheerly from loyalty.
Within the RPG spinoffs, Bowser is shown to be this to his minions, as his minions follow him of out of respect and adoration for him, not fear, despite his numerous losses. It's worth noting that Bowser is also an actual father, and there's never been any sign of turmoil between him and Junior, to the point that within Fortune Street, Bowser Jr. is the only character Bowser would never insult should he and his son compete against each other on the same board as NPCs, even while losing to him.
Mario & Luigi: Bowser's Inside Story. Before Bowser's minions notice him about to rescue them, they talk amongst themselves how Bowser would surely help them out of their situation. This is likely due to Bowser being the most competent person in their army. If Bowser simply tries to walk away and leave his minions in their cages, he'll stop and force himself to go back for them.
Super Mario RPG. He meets up with a Goomba that had gone AWOL from the Koopa Troop and had kids sometime after. Rather than throwing a fit and demanding he comes back, he acts understanding and excuses the Goomba for his running away and wishes him the best of luck, which paints him as genuinely nice to his own.
The Paper Mario series does this as well: he as an 100% Approval Rating among his mooks, and Super Paper Mario even has a mook point out that in Bowser's books, it is much less terrible to fail him and run away than it is to fail him and run away without making sure that your fellow mooks are all right first.
In Mario & Luigi: Dream Team: Following another defeat at the hands of the Mario Bros, instead of blaming it on his minions, he tells them that they did rather well and instead pins it on Antasma. This is despite the fact that said minions had gotten curb stomped by Mario and Luigi.
The Inquisitor can be played this way, at one point telling Leliana who is beating herself up over putting her people before the mission, that their people aren't tools to be thrown away. Cullen, the commander of the Inquisition military forces, also deeply cares for the men under his command and warns them not to put themselves in danger unless they absolutely have to.
On the villainous side, Samson, the general of the Red Templars and one of the two possible Dragons for the Big Bad, acts as something of an Evil Counterpart to Cullen. He becomes enraged when the Inquisitor starts killing his men and inspires genuine loyalty from them, to the point that they are willing to throw their lives away in order to help him escape, something that saddens him when he learns of it.
Grand Enchanter Fiona, the leader of the rebel mages, is another example. Everything she does, including entering a desperate alliance with the Venatori, she did so that her subordinates would not be exterminated by the Templars or the Chantry. In the quest "In Hushed Whispers," when she finds out that Magister Alexius only wanted her mages as Cannon Fodder for his army, and that he works for The Elder One, she immediately objects.
Kratos to his fellow Spartans. Even when he becomes the god of war in the second game he does not forget them and they become his most devoted and favored followers. In God of War III the Spartans stay loyal to Kratos even in death itself — it is their strength he calls upon in this game, as opposed to the Olympians in the first game and the Titans in the second.
Coronado De Cava lampshades this in Tales of Monkey Island Chapter 3: Lair of the Leviathan when he tells Guybrush and Morgan about his crew members (Bugeye, Moose, Santino and Noogie), "I may have been a stern leader, but I loved them like sons."
World in Conflict: Both Nikolai Malashenko and Vladimir Orlovsky have this trait. Malashenko often specifically refers to the men, both when praising and berating you. Orlovsky's wife writes to him saying all the women there who husbands are under his command are truly lucky because they know he cares for them, and he rebukes Malashenko sharply when he insinuates that Orlovsky isn't taking adequate steps to care for the men.
Malashenko: But these are my men lying [dead] here!
Orlovsky: They are my men too, Captain! Never forget that!
Pit cares more about the Centurions' well-being than he does his own, and the feeling is entirely mutual.
Viridi outright refers to the members of the Forces of Nature as her children.
The Witcher 2: The intro proved, beyond a doubt, that for all King Foltest's many and colourful flaws he cares about his men and they love him.
Foltest: You there! Soldier! What's your name?... Wait... Norman Sador, right?! You fought for me at the Battle of Brenna [nearly eight years earlier]! Still an arbalist?
Norman Sador: Yes, Sire. Fate has not been kind to me.
Foltest: Hah! Arbalist Sador, for your many years of loyal service to the Crown, I appoint you decurion of the arbalists!
While not at all important in the gameplay, Swain in League of Legends is said to be in the lore an incredible strategist and commander, with soldiers who survive serving under him becoming fanatically loyal while superiors request demotions just to join his unit.
General Horace Warfield from StarCraft II definitely gives off this vibe, especially considering that when he was laying on the ground impaled by a steel girder, having just lost a horrific battle against the Zerg and facing down Kerrigan, the lord and master of said Zerg, his primary concern was that she spare the retreating transports filled with his wounded men.
The Boss from Saints Row. Even at their most depraved, loyalty to their men is one of their constants, and they will repay any wrong done to the Saints a thousand times over. Just ask Jessica, who thought she could subject one of the Saints to a Cruel and Unusual Death. She got paid in full for that.
In Infernal, the commander of the HMS Liberty seems to care deeply that Lennox has killed some of his crew. It's the villainous version of this trope, since the casualties in question were incurred when Lennox was breaking out of a torture room.
William Cabot, leader of The Crew in Evolve. On several occasions he's shown to care for the members of his team, such as offering to use his connections with Hub to allow Abe to see his father again or reassuring Jack that the others will stop ribbing him once they get a chance to work with him.
Emperor Doviculous of Brütal Legend is literally a father to his men (an abusive one). Every single one of them is his own offspring. That's how you make more when you play as him in multiplayer. What do you expect from a demon king dressed in BDSM gear and voiced by Tim Curry?
Graven Ashe, the Archon of War in Tyranny can be considered this, so much as that his Archon power is to feel and heal the wounds that his soldiers receive in battle.