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.
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.
A Common staple of Ace Combat. Yellow 13 from Ace Combat 04 prided himself not on how many kills in got in battle but how he never lost a Wingman in combat. Commander Dietrich Kellerman, aka Silber One from Ace Combat Zero was this. To a lesser extent, so was Victor Vochek and his successor, Ilya Pasternak to the rest of Strigon Team in 6.
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.
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.
The RPG spinoffs of the Super Mario Bros. series, 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 (or the Koopalings).
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.
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."
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.
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.