A Crown of Stars: The Avaloni troops left stranded on Earth quickly became this: Shinji, Asuka, Hikari, Touji, Kensuke, Misato, Kaji, Ching, Bir, TJ… develop this kind of comradeship throughout the war campaign.
Advice and Trust: Hoping getting her sync rates up, Gendo commands Rei spending more time with Shinji and Asuka. As a result of it, their bonds strengthened and they became true friends and siblings-in-arms. Hurt one of them and the remainder two will ensure that you REGRET it. Bardiel and Zeruel learnt this the hard way.
Doing It Right This Time: After surviving the Angel War, dying before being fifteen, outliving the end of the world and going back to the past Shinji, Asuka and Rei are trying to save their future. As a result of this they are bonding and their relationship becoming stronger.
We may hate things about each other, but in combat we know we can trust each other with our lives.
In a very odd way, Alpha Brass and Twilight Sparkle from This Platinum Crown. He is legitimately incapable of feeling any emotions because he was so royally screwed up by Chrysalis, but during the Equestria's Strongest Couple duel it's shown that he does seem to care for her, if in a less romantic way than normal for this trope.
The pack in the ''Canisp'' series. None of them are related (except for a pair of sisters), but Meya and Canisp consistently refer to each other as "sisters". When one of the group makes a mistake that nearly kills them all and lands one of them with a broken leg and a concussion, they all stand up for him against the rest of the Wolves, insisting that it was an honest mistake and he learned from it—this in spite of the fact that one of the group spends most of her time glaring at him.
The Chance Encounter crew. Strange, dysfunctional and prone to good natured bickering, they have gone through hell for one of their friends.
Shinji And Warhammer 40 K: Shinji, Rei, and Asuka in are definitely this trope. They may have others that are close to them, they may view every human as someone to protect, but their role as Pilots has created a bond that no-one else shares. Mana even expresses frustration at how improbable it is that she will ever be a part of it, but is content that her role results in her being closer to them than anyone else.
This bond becomes incredibly important in The Keys Stand Alone, because (at least initially) outsiders don't quite grasp just how tight the four are and how much they will protect one another. Also, and again, they know they can trust one another, as opposed to, oh, everyone else.
The Malificent 11 from the Daria series God Save The Esteem will beat each other on an hourly basis, but Heaven help you if you look at (or near) any of them even slightly askew.
Also from Daria Fan Fic, The Alliance (a cadre of military cadets from the long-running ficLegion of Lawndale Heroes) was intentionally created to be this, in keeping with the academy's efforts to provide familial connections for the cadets.
The Pony POV Series naturally has the Mane Cast (which grows to include Trixie and Fluttercruel), but also has the Cutie Mark Crusaders (which ends up including Spike and Silver Spoon) and Misfit Actual (Shining Armor's squad).
While NCIS pretty much covers this already in canon, the Doorstopper fanfic "Shards To a Whole" takes the trope Up to Eleven. While the emphasis remains on the developing relationship and marriage between Tim and Abby, much of the fic centers around how the team bonds into a true family. At one point, Abby designs a Team Gibbs Coat of Arms, while in more recent chapters Ducky and his new wife Penny (Tim's grandmother) sell the newly-retired Gibbs on their idea of purchasing a run-down estate to serve as a second home for the whole NCIS team, once the team get together to restore the mansion.
Rosario Vampire: Brightest Darkness: Even after they find their own boyfriends and move on from him, the various members of Tsukune's Unwanted Harem, as well as said boyfriends, remain close friends with Tsukune to the extent that, in Act III chapter 52, he openly states that he would gladly die for them and can't imagine living without them.
Nightblade: The main cast develop into this. Nick especially relies on this because these are the only people in the world he trusts and cares about.
As in canon, we have Zoro, Nami, Usopp, Sanji, Chopper, and Robin thus far, but in an effort to avoid having his crew overpowered by Marines again in the future, Luffy has actively tried to make his crew bigger this time.
Gin is the first new addition, after Luffy thrashes Krieg…and giving implications beforehand that his captain wasn’t all he claimed to be. Gin realizes this after he loses to Sanji, and at the end, when his resolve to return to the Grand Line is finalized, Luffy extends the invitation. He accepts.
Nojiko also decides to come along to see Nami see her dream through. Well, that and to make sure she’s safe after catching Luffy and Nami in a Lemon.
Yosaku and Johnny are given an invitation when the crew is en route to Arlong Park. They accept in the end.
Crosses over with Enemy Mine above; after a couple of brutally effective Curb-Stomp Battles, as well as learning that Baroque Works’ true intentions do not aspire towards an ideal nation, three of the officer agents join the crew: Miss Valentine in Whiskey Peak and Mr. 5 and Miss Goldenweek in Little Garden. At the end of the Alabasta arc, Mr. 5 reluctantly leaves the crew to seek his own dreams, but the other two become permanent members.
Vivi also elects to remain with the crew after hearing about Luffy’s past and the World Government’s atrocities towards everywhere that he had visited, understanding that her country is still in danger and she can’t do anything about it by staying behind.
Children of an Elder God: In spite of all their fights and arguments, Shinji, Asuka, Rei, Touji and Hikari are a team and fight together during the War. After the Final Battle they think of themselves as a family.
Weiss Reacts: Teams RWBY and JNPR will stick up for each other no matter what, both within their team and for other teams.
Corrin Reacts: Corrin and his circle of friends are this, despite their dysfunctional natures, to the extent most of them team up to help Corrin hook up Flora and Jakob (thus kicking off the whole plot) simply because they're friends.
My Little Pony: Nakama is Magic: The Straw Hats and the mane six to each other, due to the latter joining the crew. Funkfreed gets in on it later on. To a greater extent, Luffy and Twilight due to him, Ace, and Sabo accepting her as a sworn sibling.
A Gem in the Rough: This story, like several other One Piece stories, uses the terminology "nakama" to refer to how the other members of the Straw Hats view each other. The author has admitted that this choice was done so as a nod to the old fansubs of the early 2000's, which popularized the term and has been a constant source of discussion in the fandom for years, as mentioned on the main page. What this story does that others do not is actually ACKNOWLEDGE that the term is antiquated within the story itself in a logical way: older pirates from the times of Gold Roger were known to use the term "nakama" for the members of their crew. This practice seemingly stopped once the Great Pirate Era began after Roger's execution. Shanks, being a member of Roger's crew, picked up the phrase and it is from him that Luffy heard it used.
Discussed in How the Light Gets in. Dean muses that as the original members of Team Arrow, Oliver, Diggle, and Felicity are this, and while Laurel considers them this and values them as family, they do not return the feeling, something Felicity herself eventually admits.
"Thing is, she still considers them her family. Despite everything. Despite every party, every family dinner, every meeting she wasn't invited to. Every time she was told to sit a mission out, every time she was put on desk duty, given different orders, she shrugged it off. Every time she was treated as an afterthought, she let it go. She loved these people. She'll love them again. She would have done anything for them. That's never been a mutual feeling. At least not in the same way."
In Dreaming of Sunshine, Team 7's bonds are stronger than in canon thanks to Shikako establishing the traditions of post-fight discussions to critique on another on each others abilities, and post-mission dinner celebrations at the Nara Residence. To a lesser extent, the Rookie Nine are all fairly close friends and acquaintances.
Their bonds are strong enough to convince Sasuke not to defect from Konoha, unlike in canon.