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Teen Titans gives us... well, the Teen Titans. Various characters within the show have referred to the Titans as a family. Their devotion to the team and each other has been proved countless times throughout the series.
Raven: (to her father) [The Titans] are my family. This is my home.
Aang calls his group "family". Since he and all of the other Air Nomads were raised apart from their blood relatives by monks, this is likely more or less his definition of family.
Toph acts like her real self in a way she probably never did with her biological family.
Azula, Mai, and Ty Lee are true companions, although eventually this falls apart--Mai betrays the true companions first, then Ty Lee sides with her, probably because Azula is a scary controlling maniac and being her true companion sucks; also notable is the fact that Mai stood up for Ty Lee against her boyfriend, who was making fun of her, and Azula who laughs at this teasing. The loss of this crew causes Azula's subsequent emotional breakdown.
These three make a pretty nice subversion of the concept, actually; one person so scary they can get people to put their lives on the line in any number of situations just because taking that risk is still preferable to dealing with that one person.
Suggested to be the case within the Southern Water Tribe; Sokka and Katara realize how they've come to see Aang as family when Bato speaks of his leaving home and latterly, his separation from the other warriors (likening them to a wolf-pack, in fact).
Subverted in Code Lyoko: in the beginning, the kids weren't very loyal to each other, and worked more like a team of convenience than friends. They never hesitated to kick someone out of the group when they crossed a line, such as when Ulrich used the Time Travel program to cheat on the lottery, and when XANA convinced them Jérémie was toying with their safety. In fact, XANA's plots frequently involved trying to break the team up, and worked quite well each time, for a while. Thanks to Character Development, though, things have changed, especially in the Season 2 finale. On the up-side, this provides a pleasant break from The Power of Friendship message that's reiterated Once an Episode in most Five-Man Band shows. It's worth noting that before coming together as a team, Jeremie and Yumi were friendless social outcasts and Aelita was trapped in a computer for ten years. Although the fact they're doing it all to help Aelita in the first place brings them right back into Power of Friendship territory. As the Flash Back episode shows, the reason they are antagonistic to Sissi is because she betrayed that trust. Otherwise, she might be a part of the group or at least a Secret Keeper.
Numbuh 1 from Codename: Kids Next Door occasionally explains to himself and others how important his friends are in Sector V:
In episode 48 "Operation: K.N.O.T.", a strange adult man named "Mooske" requests Numbuh 1 to help him take down the snake ties. At first, Numbuh 1 is suspicious of the adult, but at the end of the episode, when the other numbuhs are rescuing Numbuh 1, Mooske sacrifices himself to destroy the Queen Snake. When Numbuh 2 asks his leader who Mooske was, Numbuh 1 simply replies with "a comrade."
This is largely the whole point of Foster's Home for Imaginary Friends, with the "Foster's Five" considering each other to be family. Pretty justified, as four of them are imaginary friends, who can't technically have blood relatives, and one is the imaginary friend of the only human, who was created by said human and owes his existence to him.
Fry, after explaining the premise of the all the main characters:...do you wanna be like us, or do you wanna be like Adelai...with no severe mental or social problems whatsoever."
Also subverted once by Farnsworth:
Farnsworth: I've always thought of this company as a cheap source of labor... like a family.
Fry, Leela and Bender form a smaller group of true companions within the greater group of Planet Express.
The various clans in Gargoyles. The rather vague details about maternity/paternity may make them actual family, though it's pretty obvious that, say, Lexington shares almost no genes with Goliath.
Despite the fact that Wade is only ever seen on a screen until late Season 3, Kim, Ron, Wade and Rufus are true companions in Kim Possible.
In King of the Hill, Hank and his neighbors, even Khan eventually, are true companions, though Dale generally will only be on the receiving end of help in risky situations due to his cowardice. Toward the end of the "Not in My Back-hoe" episode, Hank touches on the difference between his relationship with his neighbors and that with his friends. Hank also treats his coworkers as true companions, but this is not reciprocated, at least not by Buck consistantly (though he does go to bat for Hank occasionally, particularly in when Hank is in a bad legal situation [assuming that Buck isn't framing Hank]).
On the other hand, Hank downright hates talking to his coworkers outside of work and wants nothing to do with their problems that aren't propane related.
The members of Dethklok all see each other as family, though only Toki ever says it out loud. While it's been stated that they have agreed never to interfere with each others' personal business, let alone take active joy in the suffering of each other (such as the effect that Pickles' brother's blatant manipulation of his wealthy sibling and family has on him), they do care for each other.
Nathan flat out confirms in FatherKlok that Dethklok is his fucked up dysfunctional family.
Considering how listless and hurt that Dethklok was by Charles' angry outbursts and unintentional neglect in Doublebookedklok (and how they could be motivated to snap out of it just by him apologizing), it's pretty much confirmed that it's not just Nathan who considers Charles an extension of the crew now.
The Freedom Fighters of the Sonic the Hedgehog cartoon are clearly a tightly-knit group of friends, all of whom have lost their actual families and so turn to each other for that kind of support; Tails even considers Princess Sally his "Aunt", and she treats him very much like her own son at times. Likewise, Sonic and Tails have a very brotherly relationship.
Chip 'n Dale Rescue Rangers: The Rescue Rangers, so much so that several episodes (including the pilot) feature one of the members leaving the group, to later return only because it's where they belong.
In Phineas and Ferb, the title characters, Baljeet, Buford, Perry, and Isabella are true companions, though Isabella has romantic feelings for Phineas. The Fireside Girls can also be considered an example. (Proof of Perry's status as a true companion: in one episode, Doofenschmirtz's 'inator of the week "will destroy ANYONE who can't make up their minds." Perry flashes back to the title characters' uncharacteristic indecision at the kitchen table that morning, and proceeds to handcuff D. to a pipe before, as usually happens, the device can be activated.")
In South Park, Stan and Kyle can be trusted to consistently treat one another like family, going to considerable lengths for one another in a variety of episodes (for example "Cherokee Hair Tampons", "Super Best Friends", "Imaginationland", "Guitar Queer-o", "Follow That Egg", "The List", "You Have 0 Friends"--you get the idea); Kyle even goes so far as to call Stan his brother in "Ike's Wee-Wee." However, they treat Butters and Kenny more ambivalently, and make no secret of their contempt for Cartman, making the dynamic between the South Park boys more indicative of two Blood Brothers surrounded by many morons.
In Adventures of the Galaxy Rangers, the Series 5 Rangers definitely fall into this, but really solidify it in "Mindnet". While the plot is pretty mediocre, the episode is a fan favorite because it is the first blatant demonstration of the team becoming true companions. Shane has been framed for theft by his fellow Supertrooper Killbane, and a Jerkass senator demands his head on a plate. Zachary tells the senator off, and a surprised Shane thanks him for the support.
Zachary: The day we don't trust one another is the day the Galaxy Rangers are finished.
After tracking down the stolen device, they're captured and Shane is forced to fight Killbane. During the bigger dust-up, Killbane sneers at his "little brother".
Killbane: You're not human, you're not a Supertrooper. Just what are you, Gooseman?
Shane: I'm a Galaxy Ranger. Make sure you never forget that.
Mindnet also marks the first time the Rangers "pool their badges" in a Mental Fusion tactic that is used occasionally throughout the rest of the series. Zachary is very quick to fall into the Team Dad role, especially when it comes to the parent-less Niko and Shane. Fanon states that his true-companion relationship with the Rangers is what has kept him relatively sane after the loss of his wife and his rebuilding into a Hollywood Cyborg.
Mystery Inc. from Scooby Doo. For that matter, any of the "gang of teenagers solving mysteries" genre shows that sprouted from the success of Scooby Doo.
It could be said that the original seven of the DCAU's Justice League are true companions. They would have to be after all they've gone through together.
A great example of it this is Flash's Day in The Limelight episode of Unlimited. Flash is able to convince Batman to come to the opening of his museum with little more than a "please," and delivers a breif but touching "you don't understand at Orion, who straight up asked how he can put up with the Flash's antics and methods.
Most of the combiner groups in Transformers Generation 1, but especially the Aerialbots and the Constructicons. For a group of villains, the Constructicons have had scenes together that are downright touching. Omega Supreme was also a member of the Constructicons' crew back in the days before Megatron used his Mirror Morality Machine on them; now he's their sworn enemy. The Combaticons may not qualify though, since although they work well together (particularly when all the world is against them), they were thrown together purely by circumstance, and Swindle has no loyalty to them at all (he once literally sold the others for scrap!).
Team Prime is definitely this. Arcee even refers to them as "family".
Pepper Ann: Ann, Milo and Nicky are always there for each other even though PA's crazy schemes get out of hand sometimes.
The Rugrats babies are pretty much always together, and it's often hard to believe that the in-universe time the series takes up would have to be less than a year or two. Even Angelica is included.
Twilight Sparkle, Spike, Pinkie Pie, Applejack, Fluttershy, Rarity, and Rainbow Dash. It's a series about The Power of Friendship. They may fight sometimes, but it's crystal clear that no matter what, there's no way they're abandoning one another.
In The Super Speedy Cider Squeezy 6000, takes this to its greatest height yet. During the competition for the farm, Applejack allows the others to help her and her family. Why? Because she now considers them her family.
Sweetie Belle, Scootaloo and Apple Bloom, who bonded for a mutual reason to form the Cutie Mark Crusaders.
The members of Young Justice, as exemplified in the episode "The Usual Suspects", where Superboy, Artimis, and Miss Martian each admit to keeping major secrets from the rest of the team and are immediately forgiven.