A Crown of Stars: Although Asuka can hardly bring herself to believe it, her future tells her that she and Shinji will end up like this. When they showed up they smiled happily and looked absolutely inseparable.
The Child of Love: After enduring plenty of trials and pains Shinji and Asuka end up getting married and leading happy lives. In the epilogue and side-stories they are depicted as still very in love, supporting each other and drawing strength from each other.
Misato and Kaji get married when he returns from Instrumentality. They get along pretty well.
Shinji and Asuka. They have troubles, arguments and fights but they are happy together.
HERZ: Shinji and Asuka. Their relationship has gone through bumps and hardships and has needed considerable healing, forgiveness and soul-searching on both parties, but they are happy together.
Higher Learning: Kaoru told that, even though they had troubles and hardships, Asuka and Shinji were very happy together after getting married in his timeline.
The One I Love Is: Shinji and Asuka got married in the Epilogue after living several years together happily.
The Second Try - After Third Impact Shinji and Asuka were forced to overcome their many issues and traumas and work together. In the process they fell deeply in love, finally got married, and had a daughter.
Dr. Watson and Sally SparrowMeet Cute in "Watson and Sparrow" and go on to marry in the next episode. They remain very in love and very devoted to each other, especially as Sally gives up her life in the 21st century to be with Watson at the close of the 19th. Sally gives birth to a daughter who turns out to be a Time Lord, and the couple eventually have more children. Even Holmes, in the end, is grateful for Sally and the children, attaching himself wholeheartedly to his best friend's family.
Beth Lestrade, on the other hand, has no less than a Trauma Conga Line in her relationship with Sherlock Holmes, but she earns her happy ending and marries him before returning to her own era. When the couple are reunited at last, they still have some issues to iron out, but their long separation has only deepened their appreciation for each other. Beth has commented that they will probably never get off the honeymoon, and both are perfectly fine with that. Now, They Fight Crime! in the 22nd century, particularly dealing with the clone of Professor Moriarty.
In Marks of Time, Meredith and Gilorn. Also, Caleniel and her husband. The worst moment is a brief argument between Meredith and Gilorn in chapter 2, but they quickly apologize and forgive each other.
Fleur De Lis and Fancy Pants in Of Lilies and Chestnuts. When Fancy learns that Fleur is infertile, his first act is to comfort her in her despair for a few hours and suggest adopting a foal so Fleur can salvage a glimpse of her dream. Fleur adores her husband in return.
From the Gensokyo 20XX Series, we have Ran and Ren, after being engaged for at least four or five years, sticking by one another through thick and thin, never at all arguing or doing anything to hurt one another. Sadly, after enjoying a rather happy marriage, Ren passes away and Ran is a left a grieving widow.
Meg's Family Series has Meg and Zack. Despite all the problems (Including Abusive Parents) that they've gone through they still love and care about each other. It helps that Zack is extremely protective of his wife.
Spike and Rarity eventually became this, after much Character Development on Spike's behalf, and mutual exploration of why the two would be attracted to one another in the first place.
Meanwhile on Remnant, Jaune Arc and Pyrrha Nikos eventually got married, though only after adopting their teammates and Pyrrha's core canon death.
In the Arrow series Legacy, Oliver and Felicity have been married for over twenty years. Their kids still catch them having tickle fights in the kitchen sometimes.
The One Piece fan fiction series Rerum Danarae has Borsalino note Admiral Kizaru and his civilian wife Suikô (水光, water light), who, despite being married over twenty years, still play rather elaborate light-BDSM games; it is implied that Suikô controls her husband's antics by banning him from the house. There is also Fleet Admiral Kuzannote Admiral Aokiji, who, contrarily to his former lifestyle as a vagrant of the seas (who from tradition never say no to being propositioned by their preference), hasn't had eyes for any other woman but the one he later married – Kumori C. Theodora – since meeting her 28/31 years ago; the pair has to date four children, and is, after 25 years of marriage, still raunchy to the point that their youngest daughter Evermist lampshades this in protest.
Arguably the case for the Official Couple of The Bug Princess. It's not a question of whether or not they're happy (they are); it's a question of whether or not they're actually married.The union was cemented via Magically Binding Contract, but it's technically only valid in the Neitherworld. Steps are taken to also make it legal among the living.
Young Justice Titans has this starting to develop with the senior members of the old team who decided to marry young. Namely, Superboy and Mrs. Martian as well as Artemis and Wally West. Mrs. M and Conner have most of of their old issues worked out, and are now happily raising not only a kid but mentoring now as well. Artemis and Wally meanwhile are in semi-superhero retirement, focusing on raising their daughter, and while still annoyed by each other, genuinely love and care about each other without reservation.
This in fact is discussed in part during one part, where Rapunzel hearing about the durability of a troll's marriage through all the bumps muses that this is only further proof for her that she and Eugene are in genuine love.
In The Sanctuary Telepath (in the universe all of them stays alive, at least) Janine and James eventually become this - supported by a century worth of common history. They're very much in love, trusting, in sync, and with Janine's brother they form the London Three.
In the Kung Fu Panda fic The Vow, Lord Shen's parents, Lord Goa and Lady Jing, are this. Before Shen's Face–Heel Turn, he and Lady Lianne are looking forward to being this as well. They ultimately manage to be this after so much pain.
Contrasting with the awful lives they live in canon, A Spark of Ice and Fire has the marriages between Sandor Clegane and Tysha, Stannis Baratheon and Lynesse Hightower, and Tyrion Lannister and Agatha Heterodyne. Tysha's warmth quietly mellows out the Hound; Lynesse, despite being very much a Gold Digger, has an excellent head for business and respects and genuinely appreciates Stannis; and Tyrion's political skills blend perfectly with Agatha's genius.
The Pieces Lie Where They Fell: After hints were given in the first story, the sequel Picking Up the Pieces reveals that Sweet Surprise is and has been happily married to a firepony stallion named Hot Rod and a psychiatrist mare named Sound Mind (who actually made a short appearance in the first story) for going on five years, much to the surprise of her fellow Captains when they find out. The pair demonstrate this when they separately come into her office later on because they're worried about her.
Son Of The Sannin: After living for a few years under the same roof while raising Naruto together, Jiraiya and Tsunade eventually develop feelings for one another and get married. While they do still bicker from time to time and have some issues, they end up a very happy couple overall.