Within the organization, there are some stronger bonds among specific teammates. Batman, Superman and Wonder Woman are especially close (at this point multiple mainstream incarnations of Superman and Wonder Woman have been romantically involved, with numerous alternate universes having them marry and even have children, on the other hand). Green Lantern (Hal Jordan) and Flash (Barry Allen) are close friends as are Green Arrow and Green Lantern.
Y: The Last Man: Yorick, Dr. Mann and 355 (despite their conflicting personalities) and later Rose; plus the all-girl group of Hero, Beth II, Natalya and Ciba.
Marvel's Agents of Atlas. Their true-companion bond is Lampshaded in their original miniseries, with super-spy Jimmy Woo as the group's leader.
The Runaways team originated as six kids who discovered that their parents were actually supervillains, and banded together to try to stop them. The main cast did suffer dramatic changes, though, such as the revelation of Alex as The Mole and his subsequent death, Gert's death, and the additions of Victor, Xavin, and Klara.
Transformers: The Autobot special forces team known as the Wreckers, particularly concerning its seven core members (Springer, Broadside, Sandstorm, Twin Twist, Topspin, Roadbuster and Whirl). Possibly the Insecticons as well, in that they're a trio of freaks despised by both Autobot and Decepticon and are really only loyal to each other.
Watchmen: Rorschach and Nite Owl II have this sort of bond. In fact, it could be argued that Rorschach sees all masked superheroes as true companions, given that he warns them about a potential mask killer at the beginning of the book, even though he doesn't much care for most of them on a personal level.
"An attack on one is an attack on all of us."
In Before Watchmen: Minutemen, there is the bond between the original Nite Owl, Mothman, and Silhouette, who decide to team up apart from the Minutemen to fight against the kidnapping and exploitation of children. When Ursula is outed as a lesbian, Hollis and Byron are the only two willing to vote against her expulsion from the Minutemen, and part of Hollis Mason's original goal behind writing his memoirs is to expose how the Minutemen's leadership threw Silhouette under the bus to distract people from their own sins.
The gladiators with whom the Hulk formed a Warbound pact in Planet Hulk; they even joined hands together like in the page picture up top. Warbound are new families forged in conflicts, with whom teamwork and understanding are the only ways to survive. This is made all the more significant given that each member of the Warbound has lost their actual family, as Miek saw his entire hive slaughtered before him, Korg was forced to kill his own brothers in the Maw, Hiroim was exiled for breaking a previous Warbound pact, the Brood was separated from her sisters, Elloe's father was killed by the foreman of the Maw, etc.
Any crew that includes The Hulk is doomed (Defenders, The Pantheon). True companions that fight him fare better, which may be why The Avengers outlasted his membership in it.
The various teams of X-Men display this trope at times.
The strongest group is probably the 80s X-Men: Cyclops, Jean Grey, Colossus, Storm, Wolverine, Nightcrawler and Kitty Pryde.
Most of these characters were orphans, exiles, and outcasts. The X-Men became their surrogate tribe. That they did not look like a natural family served to underline the idea that these people chose each other.
The Fantastic Four would qualify as well, if three of its four charter members weren't already directly related by blood or marriage. The extended crew includes Spider-Man, whose Vitriolic Best Buds friendship with the Human Torch dates back to the character's first few issues. He's since become such a part of the family that he's considered Franklin's Honorary Uncle, and has taken Johnny's place on the team following his death (with Johnny hand-picking him for the spot via Video Will).
Some versions of the Brotherhood would qualify, specifically Mystique's group. With the exception of Blob, they are all good friends that look out for one another, and show unswerving loyalty to Mystique.
The various Teen Titans teams in the comics are just as much a surrogate family as the animated version. This is especially true of two teams: the "original 5" (Robin/Nightwing, Wonder Girl/Troia, Kid Flash/Flash, Speedy/Arsenal/Red Arrow, and Aqualad/Tempest) and writer Dan Jurgens' team (almost all of whom were the children of women impregnated by an alien species, the H'san N'atall). Arsenal's late daughter Lian constantly referred to the various Teen Titans as "Aunt ____" or "Uncle ____" just to illustrate how close they are, but she also had the privilege of knowing all her "godparents" REAL NAMES.
This is how the Justice Society of America is set up as well. The four statesmen of the team (Hawkman, Wildcat, Flash I and Green Lantern I) have all lost children or otherwise had problems being fathers, as elaborated upon in the "Princes of Darkness" arc. Many other characters have parental issues, such as Jesse Quick/Liberty Belle II (dead father), Hourman II (absentee father returned from the dead), Stargirl (stepfather is crimefighting partner, father is a dead criminal) and Damage (son of the original Atom, created by Vandal Savage). Ma Hunkel, the original Red Tornado, is the maternalglue keeping the team together.
Frank's gang from Mini Monsters is a good example: Sure, they don't like each other at times, but it's clear that they love each other deeply and stay together regardless. Victor's relationship with them is a case of Fire-Forged Friends (Piruja too, but in a much lower manner).
Many of the Avengers teams over the years have been effectively true companions. One good example is the nearly-first lineup: Captain America, Iron Man, Thor, Giant-Man, and the Wasp. (The Hulk was a founding member, but quit almost immediately, with Cap taking his place.) All five were practically in tears when they first parted ways, even though they'd only been together for a dozen issues.
Of all the ties formed in the Avengers' long history, none match those between Captain America, Iron Man, and Thor. The team is always at its strongest when these three are in it, and any two of them would lay down their lives for the third without hesitation. This is what made the Cap/Iron Man conflict in Civil War so devastating; one has to wonder if it might have been averted if Thor hadn't been dead at the time. The adverts for Avengers Prime put it best: Many have answered the call, but three have always stood above the rest.
It's also why Thor is so fucking pissed at Tony when he finally does return. A man he considered at least as close as a brother not only turned on people they both called allies (especially Cap), but then cloned Thor without permission. I doubt any of Loki's many betrayals hurt Thor as much as that did.
Likewise, the three main members of the Invaders (a World War II-era group consisting of Namor the Sub-Mariner, the original Human Torch, and Captain America) are true companions. They might not always like each other, they may be on different sides of a fight sometimes, but they have a bond that can't be broken.
Way back in the almost-prehistoric days of the Avengers/Defenders War (which may be the first big Marvel crossover), it is the bond between Captain America and Namor that brings the two teams to cease hostilities. Interesting to note that this occured prior to the creation of the Invaders series and its subsequent Retcon.
Several of the Avengers members are related by blood, marriage or through more complex links. For example, Hank Pym has been married to Wasp and has had romantic relationships with both Tigra and Firebird. He is also the creator of Ultron, with Vision, Jocasta and Alkhema as de facto grandchildren. All three being artificial versions of other Avengers: Wonder Man, Wasp and Mockingbird.
Thunderbolts usually subverts this. Jolt joined the team thinking she had found a second family after her parents were kiled. Turns out they're super villains who try to take over the world. Then they turn on each other and try to kill each other. Even when the individual members of the team admit the team is like a family they still betray the team later.
The Young Avengers started referring to themselves as a family soon after the death of Teddy's adoptive mother. The Children's Crusade miniseries seems to be cementing this.
Then The end goes and ruins that.
The Flash's Rogues Gallery, the Rogues, are probably the closest knit collection of villains in comic book history. They aren't an official team (most of the time) but they all stay in touch, throw reunion parties, look out for each other when they can, and are generally as close as friends can be. After the death of Captain Boomerang, Captain Cold starts arranging his funeral immediately, and when a young punk starts mocking the late Captain Boomerang, Cold straight up decks him without warning.
The Filipino newspaper and web comic Beerkada follows the hijinks of a group of young Filipino adults who are true companions. In fact, the title of the comic is a portmanteau of "beer" and "barkada," which is essentially the Filipino equivalent of true companions.
The long-running Italian series "Comandante Mark" (1965-1999) by Giovanni Sinchetto, Dario Guzzon and Pietro Sartoris, featured a basic unit. The series takes place during the American Revolutionary War. Comantante Mark is a French-American captain of a revolutionary group. His group includes main love interest Elizabeth "Betty" Gray, his right-hand men Mister Bluff and Gufo Triste (Sad Owl), and the hound Flok. Mark and Betty are in their 20s, the other two are middle-aged. Mark and Betty often argue, particularly due to his tendency to be overly affectionate with other women. Mister Bluff is a lifelong adventurer, former pirate, womanizer and eternal optimist. Gufo Triste is a Native American warrior, proud of his cunning and a couple of rarely used magical skills. He tends to be pessimistic, cynical and openly disdainful of women (with a soft spot for African-American women). They are best friends but constantly argue on their belief systems. Flok is extremely loyal to Bluf and loathes Gufo Triste. Yet throughout the series and despite their near-constant arguments, the characters consistently risk life and limb for each other.
In one Knights of the Dinner Table storyline, Sara temporarily joins her boyfriend's gaming group, only to get constantly sidelined and then overhear that they only wanted her for a mixed-gender bonus at an upcoming tournament and planned to get rid of her afterwards. Later, the guys show her pictures of the Humiliation Conga they inflicted on the other group in retaliation — behavior that would normally appall Sara, but which she instead finds touching because it's a sign that she's fully "one of the guys" (and because she's understandably ticked off at her ex-boyfriend).
In a rather unique exception to all the strictly superhero teams in comics, the core staff of the Daily Planet — especially the foursome of Perry White, Lois Lane, Clark Kent, and Jimmy Olsen — consider themselves to be like family to each other. Of course, Clark is also part of the group that forms the group of JLA members that joined up before the new recruits/replacements but after the founding members, which just separates his two identities even more.
In addition to the Secret Society, there is their opposition in the Secret Six whom have formed such a strong family bond that, even after Mockingbird leaves them, they still stay a family.
In Gold Digger, Julia Diggers and her students are like this. Do not harm them and let her find out about it, or you're in for a world of pain. Also, the three wererats in Throne Of Shadows were specifically raised to be able to trust each other completely, an advantage that wererats almost never have in life.
Peter Parker always had allies in Ultimate Spider-Man but it wasn't until near the end of the first comic's run did he gain True Companions in the sense detailed here. Fellow super heroes Johnny Storm (the Human Torch) and Bobby Drake (Iceman) moved in him with him and went to his school. Even all of his ex-girlfriends, Mary Jane Watson, Gwen Stacy, Kitty Pryde (Shadowcat), put their differences aside and became great friends. Peter's Aunt May was part of the group, too! (After all, she was letting all of the kids live her house.) They worked, lived, and fought together. They were together until the bitter end...
Tintin, Haddock, Calculus, Thompson, and Thomson would all qualify - as well as the various side characters they meet in stories, such as Chan.
The village of indomitable Gauls in Astérix are all True Companions. In many comics, it seems that all of Gaul is that way.
The Anti-Megalosaurus Force in Godzilla The Half Century War, espeically Ota, Kentaro, and Colonel Schooler, who are all present from the first issue. By issue three, they've been through nearly 20 years of life-threatening combat together and are practically family to each other. Kentaro in particular makes the choice to stay in the AMF instead of pursuing a safer line of work just so he can have Ota's back.
In H'el on Earth, H'el was like family to Superman's birth parents, Jor-El and Lara-El. The day before he was sent into space, they gave him a copy of the family crest; making him an honorary member of the House of El. Subverted in the H'el one shot leading into Krypton Returns, which reveals this is completely untrue, and is simply something failed science experiment H'el convinced himself of to give his life meaning.
The Holo Brothers are members of three different alien races. They were all orphaned too young to remember their birth parents, and grew up together in an orphanage. Now adults, they still consider each other brothers and act as if they were actually members of a single family.
Transformers: Robots in Disguise: Soundwave and most of his cassettes are close. Soundwave was found, a lone mentally ill derelict out on the street, by Buzzsaw Laserbeak and Ravage. They taught him to control his super senses which were causing Sensory Overload, and he treated them as equals, even though they, both as data discs and animalistic bots, should be lower than him. When Rumble and Frenzy were refitted to work with him, they joined the fold, sticking with him in the present, and even displaying the nobody get's left behind mindset back in Transformers Autocracy.
The Guardians of Kandrakar in W.I.T.C.H., both in the comic and the animated adaptation. Takes them a while, but by the time of the third saga they're practically family.
Hit-Girl with Kick-Ass, after her dad died. He's pretty much the only person she opens up to at all, and cares dearly for his well-being. He's also her go-to sidekick in the second volume.