If you're a Super Villain, it is a very, very, very bad idea to hurt a member of the Justice League when Superman's around. There's a reason he's the default leader of the team.
Just about every leader, or just high ranking member, of the X-Men is this.
Xavier, the founder, was a surrogate father to both Scott and Jean, as well as everyone else in the original five, he cares deeply about them and their safety, with one issue showing, in detail, every person Xavier let die and show how it effected him emotionally.
Cyclops, while this is often ignored or not noticed, has a tendency to be protective over new members, and often acts as Team Dad when around younger members. He may generally suck at social interaction and he failed his actual son (though, in fairness to him, he didn't intend to abandon him the first time, and eventually he had to give him up to save his life), but when it comes to his team, he'll bromance with the older ones and do his best to keep the younger ones safe and prepared. Special mention should go to his treatment of the early-mid 2000s class (especially Pixie, Rockslide, Nori, and Anole, and to a lesser extent X-23), with it being him who noted they should reach out and try to take better care of them. Though, this depends on the writer and how they want to treat Cyclops.
Emma Frost is a MOTHER to her men, having been devastated to the point of a Heel-Face Turn when her Hellions all died; she expresses this by her care for her young students, such as Gen. X, New X-Men, the New Hellions, etc. Special note is her care for Jullian Keller (Whose codename, Hellion, was picked for her original team) and Noriko/Surge. She once usedMind Rape on a villain who threatened her students by removing the only positive figure from their memory, effectively causing them nothing but emotional pain for the rest of their cold existence.
Logan, while not a leader, is almost always a father figure to young, especially female, X-Men. When placed in charge of X-Force, he takes special care over the other members. (This is probably because two of the members are only in their late teens-early twenties, while the fourth is his own child/clone who is no older than 17.) There's a reason he has one sidekick per generation.
The love Doctor Doom feels for the people of Latveria is the one thing that is stronger than his hate for Reed Richards; he would gladly lay down his life or even (temporarily) ally with the Fantastic Four to protect them.
Captain America. Any team he gets put in charge he treats like his family, possibly because of his late Sidekick Bucky.
Nick Fury during his more sympathetic moments. Special Mention to the Seige event, where he makes special attention to make it very clear that the plan to stop Osborn was his idea, so that if all fails, only he will be arrested for Treason.
The High Evolutionary tends to treat almost everyone in a rather paternal way, but he looks upon the Knights of Wundagore moreso than others. (And seeing as he created them, one could say that he is their father.)
Papa Smurf is pretty much this to The Smurfs. In fact, in the English vocal track of the live-action movie, Gargamel goes so far as to have Papa Smurf say he has 99 sons and one daughter. Papa Smurf himself says that they're his family.
And as he claims in the cartoon, Grandpa Smurf was exactly the same when Papa Smurf was a young smurf.
Reed Richards of the Fantastic Four is the father of his team. Given that their entire thing is that they're a family of superheroes, this is basically his thing, besides being The Smart Guy above all Smart Guys in the Marvel Universe.
Erico's fanverse for Mega Man features Doctor James Cain of the Maverick Hunters, who the troops revere as a father. For some, such as X and Zero, he's the closest thing to a real father figure they have.
Battle Commander Karrde in Tiberium Wars is deeply concerned about the welfare of the troops under his command. At the same time, he also has to grapple with the necessity of ordering men to their deaths and making battlefield decisions that result in victory at the cost of his troops' lives, which forms a major part of his character's personal conflict over the course of the series.
Dragon Age The Crown Of Thorns has the dwarven noble protagonist during his brief time as Commander, before his deliberate Zero Approval Gambit. In fact, even though said gambit is executed flawlessly, his men, or at least one very high-ranking military figure, never believe in his guilt, to the point where said high-ranking warrior threatens the Assembly with leaving for the surface, along with his whole house, unless they give the prince a trial, which they do, much to Bhelen's chagrin. What makes this even more interesting is that they were all proven right when Trian, who is still very much alive, revealed himself.
It's not uncommon in The X-Files fics for Skinner to be cast in a substitute-father role to Mulder and/or Scully, and Scully's mother, while a civilian, frequently mothers Mulder as well.
In the Avatar: The Last Airbender and Manga/Naruto crossover Bodyguard of Azula, Naruto is this to a huge part of the Fire Nation Army, to the point that they beg not to fight him when he is buying time for Azula and Zuko to escape the capital, and try to let him out of the prison when he surrenders. He plays this trope again by ordering them not to do it, since all of them would be killed if it failed
In the Star Trek fanfic Heroes, Spock regrets that Surak will never see the side of Kirk that becomes upset whenever a crewman dies.
Used in K19: The Widowmaker: Mikhail Polenin, the first captain of the K-19. All his men love him, he takes an interest in them and is a great submarine captain... then five minutes in, he's demoted and replaced by Alexei Vostrikov, who is a drill-obsessed hardass. Not only do the men hate him because he overworks them, they feel that their "rightful" captain has been wronged.
Almost called out by name when the Vostrikov is incredulous that the sub's crew would bring their fears directly to his predecessor.
Polenin: A crew is like a family. The captain is the father.
Russell Crowe seems to play these characters well. The Roman general he played in Gladiator cared deeply for his men, and in some ways even more for his fellow gladiators. Captain Jack Aubrey in Master and Commander is this even moreso.
In Apocalypse Now, Captain Willard (Martin Sheen) alludes to Lieutenant-Colonel "I love the smell of napalm in the morning" Kilgore (Robert Duvall) as falling into this trope. Arguably he comes across as more of a Cool Uncle or Older Brother.
The Captain in Das Boot is very much like this, although he is only thirty years old and the men are in their late teens.
Captain Staros in The Thin Red Line. His parting words to his men are: "You've been like my sons. You are my sons."
General Robert E. Lee in Gettysburg. Exemplified in one scene shortly after the titular battle, where Lee apologizes to his men for their defeat at the hands of the Union army and takes all the blame for their failure. His men, on the other hand, refuse to blame Lee and plead with him to send them back into battle to redeem themselves.
General Kuribayashi from Letters from Iwo Jima tries to be this, but the other officers in the army have the soldiers still be Red Shirts, and the only one this has good effect on is Shimizu.
In The Rock, the "being torn up about sacrifices" part leads Brigadier General Francis Hummel into the villainy. It's notable how everyone even remotely knowlegeable still talk all respect about him even after he initiates a hostage/terrorist plot. Which he intended to be just a bluff.
Col. Keith Davenport, 12 o'clock High. So beloved by his men that after he is relieved of command and Gen. Savage replaces him, EVERY pilot in the group requests a transfer out of the 918th.
In After Earth General Cypher Raige is respected and looked up to by his fellow rangers, including one who was apparently saved by him from an Ursa.
In Starship Troopers LT Raschyk demands the best, and gives the best (it's implied the "beer and entertainment" isn't something most platoons receive).
In The Hunt for Red October Captain Ramius stationed many of his former officers on the Red October and they are willing to risk their lives to help him carry out his plan to defect with the submarine to the USA. One of his officers even takes a bullet for Ramius.
Manhua and Manhwa
The majority of the generals in Ravages Of Time but subverted with Lu Bu who, while extremely talented, thinks of his soldiers as nothing more than disposable pawns.
Ha Jinsung from Tower of God is a villainous version, as he dotes on his student and subordinate Viole like an overly embarrassing father.
The eponymous character of Dispatch's "The General".
Abraham, a father to his people and at least four ethnicities (at least two of which are extant).
Lets not forget God. All of his followers are his children. He guides and comforts them, and some believe he even died for them.
In The Book of Mormon, Captain Helaman's 2000 young soldiers call him "Father", and he refers to them as his sons.
Table Top RPG
Iron Kingdoms: Captain Phinneus Shae, pirate captain of the Talion. As his crew are all outcasts and wanted by the Cygnaran army for mutiny, he is willing to kill himself against an undead captain, to keep his crew safe.
Cyrano de Bergerac: This trope is Deconstructed by Carbon de Castel-Jaloux attitude(see the quote of Sun Tzu in literature above): He is the captain of the Cadets of Gascony, a nobleman who pays his own company, so he only is obliged to obey his superiors in military matters. He is troubled at the Siegue of Arras, because all his men (to whom he refers as his sons!) are starving. His superior, The Marshal of Gassion, Count De Guiche, asks him to punish his men for disrespecting a superior officer (himself). Using his prerogative, Carbon de Castel-Jaloux chooses not to. After that, De Guiche informs him that his company is the bait in a gambit that can win the battle. Carbon de Castel-Jaloux is completely willing with the plan to send all his company to death because that is what a Gascon soldier is supposed to do. Notice that if he has punished his men – soldiers in an army are supposed to respect a superior, no matter how despicable they found him - his company would not have been picked to fight a suicide mission.
In All My Sons, Chris's Army nickname was "Mother McKeller." While little is said about his commanding abilities, he respected and was respected by his men, and was prouder to see them fighting selflessly and dying honorably (almost all were lost) than of going back to work with his father, where civilians hadn't changed their old money-grubbing ways.
Hiroshi Kirisawa, the leader of the Special Investigations 2nd Unit in Metro PD: Close to You, is frequently credited as the entire reason that the Ragtag Band of Misfits that makes up the unit is able to function at all, let alone as the well-oiled machine that it is. He's charismatic and dependable, encourages his men to run their investigations as they see fit, and is always prepared to back them up or take responsibility for their fumbles. He looks out for his guys off the job almost as much as he does on, doing things like regularly having the whole team over to his place for a home-cooked meal since most of them are bachelors who can't or don't cook for themselves.
The Order of the Stick: When standing between Miko and Belkar, Roy says that he learned in school that the commander does not abandon one of his people in the face of the enemy. He was at one point seriously considering not rescuing a captured Elan, but ultimately decided that this was unbecoming of him.
Schlock Mercenary Captain Kaff Tagon cares for and takes care of his men this way. And insulting him is a good way to get a faceful of fist from the men