Advice and Trust: Although Shinji and Asuka hooked up at the beginning of the story, and their relationship gave them an emotional anchor to cling to when things got too tough, the story made clear that they would have to fight and struggle to get a happy ending. And it was made clear as soon as Leliel absorbed Asuka in lieu of Shinji in the next chapter. Moreover, now they have a deep bond with Rei and have a better relationship with their friends, they have to protect more people.
The Child of Love: Shinji and Asuka had to work hard to get their happy ending. First of all they had to learn to stop fighting and reach each other out. Then they had to go through Asuka’s pregnancy. Then they had to stop Gendo’s plans which might mean Asuka’s death and Teri being turned into a living tool war. THEN they had to beat the remnant Angels AND SEELE and at the same time raising their baby.
Children of an Elder God: The main characters got to fight and slay Cthulhu MythosEldritch Abominations to have a chance to lead a mostly happy life. this is most evident for Ritsuko and Maya. The former awakens from a 500-year-long coma, where she has been watched over by the latter all that time. Ritsuko is still a mermaid of sorts who can't breathe air, but Maya assures her that it might be possible to make her human again. Regardless, they can finally live their lives together again.
A Crown of Stars: Shinji and Asuka are literally granted divine intervention to help them, but they still have to work to fix their troubles. Your relationship is a mess? Talk and open up to reach each other out, to try to understand and forgive each other and work on rebuilding bridges. Your world is a hellish, post-apocalyptic wasteland? You will have to fight the tyrants lording over the starving masses and then help to rebuild.
HERZ: Despite everything that they had to endure during the Angel War the main characters still are forced to defeat SEELE once and for all if they want to lead happy lives.
Evangelion 303: The history seems being going for this. The characters suffer traumas and struggle to overcome them and fix their troubles throughout the fic.
Shinji and Asuka's relationship goes through many troubles while they try to figure it out. Right when it looks that it is getting somewhere, some disaster happens and it gets worse. However they ultimately manage to solve their troubles, connect with each other and get engaged.
Commented by Kaworu in one scene. He told Shinji that everyone go through trials in order to achieve happiness.
Last Child of Krypton: Though there is a great deal of hardship, ultimately the story ends a whole lot better than canon.
In Neon Genesis Evangelion: Genocide, Shinji and Asuka had to get over their issues, fight new battles, survive another war, and leave their homeland together with their family and friends in order to get their “happily ever after”.
Scar's Samsara: Pretty much the entire story is about Scar having to earn his redemption after he murders his brother, with a large part of the tension coming from the question of whether or not this will actually happen.
Scar Tissue: This fic is very dark, with all characters (Shinji, Asuka, Misato, Ritsuko...) making awful things or grave judgement lapses and then regretting them and seeking atonement and expiation for them. However it looks like if there will be a light at the end of the tunnel.
Fallout: Equestria is much darker in tone than the Fallout games are. While the story can be extremely depressing it does make the end that much better.
The premise for Blind shows how much work Naruto and Hinata have to do to end up happy. So...(deep breath). Naruto almost watched his best friend (Hinata) get her eyes gouged out at the age of 3 and has made it his mission in life (second being become Hokage) to getting them back. He, unfortunately, is only a genin and has 4 years to do so or Hinata is either A) branded with the Caged Bird seal or B) disowned and exiled from the clan. To compound the problem he ends up a missing nin with kill-on-sight orders for 3 years.
Hinata has to deal with what's mentioned above but gets put in a coma where she's slowly dying but saved in the nick of time only to hear your best friend has just gone AWOL and the Hyuuga elders are preparing to seal you and time's running out to get your eyes back. Man do they have it rough.
The Chip 'n Dale Rescue Rangers epic fancomic Of Mice and Mayhem puts the characters through about as many hardships as would be possible without betraying the essence of the original show and characters. Against all odds, things work out for the best.
Even with all the madness and downright cruelty in the Axis Powers Hetalia fanfic All He Ever Wanted, Austria was at the receiving end of some the worst abuse to the point of being forced to see his beloved Hungary raped by Prussia. He also happens to have one of the better endings compared to the other characters.
The Hill of Swords ending has Shirou, after 5 seperate resummonings, and who knows how many years finally reuniting with Saber in Avalon.
This trope is essentially the center point of the Pony POV Series. While it hasn't ended, even the ends of story arcs tend to lean this way. The two Sixth Rangers especially had to go through Pony Hell to get to the point where they're genuinely happy with their lives. In the case of Fluttercruel, she literallywent through Pony Hell!
This is especially a plot point in the Dark World Series, where the heroes not only have to defeat Discord, but also redeem themselves after a thousand years as his minions and defeat Nightmare Paradox, who's worse than Discord in every way. Ultimately, they are successful, though they get a Bittersweet Ending: Pinkie Pie and Fluttershy die, and refuse the one time offer to come Back from the Dead, while Twilight becomes the Concept of Happy Endings and has to move on to aid other worlds.
The epilogue of Ace Combat: The Equestrian War ends the story on a bright note. Equestria is slowly being rejuvenated by the power of the Elements of Harmony and the magic of Princesses Celestia and Luna to a state before the war. Rainbow Dash becomes a honorary member of the Wonderbolts. Derpy adopts Pipsqueak and Firefly stays in Equestria. She also becomes Rainbow's older twin sister (though they are actually cousins).
Inner Demons: Since the basic premise is Twilight Sparkle being consumed by her inner Darkness and becoming Ax-Crazy and mentally and physically tormenting her former friends as part of her quest to become Equestria's Evil Overlord, it figures that the protagonists have to go through Tartarus (literally, during the Final Battle) to stop their friend and save her from herself. In the end, Twilight is not only saved, but even becomes a Princess alongside Celestia and Luna. Plus, ultimately the only death in the story is Trixie, and even then, her spirit assures Apple Bloom that she died content.
The Immortal Game, being a War Fic, has the Mane Cast going through hell, some of them nearly going crazy and all of them losing their innocence, all to defeat Titan and save their world. In the end, they're successful and like Inner Demons above, Twilight even becomes an alicorn in the process.
The New Retcons have Elizabeth and Anthony from For Better or for Worse go through this, working through an insane mother(in-law), them realizing who they married is not who they thought they married, Elizabeth cheating on Anthony and foisting a bastard son on him, Anthony's undiagnosed Aspberger's, Elizabeth's feelings of inadequacy as a woman but unwillingness to change it, and the death of Elizabeth's mother as well as discovering that Anthony's father killed his mother. They eventually find happiness with them staying together and settling in Vancouver. Especially interesting in that early foreshadowing hinted that they would divorce, when in fact it was her brother and sister-in-law who divorced.
Speaking of said brother, Michael had to do his own happy ending earning: working through the same insane mother (who more directly affected his family since she terrorized them), his workaholic tendencies, two miscarriages, an autistic son, a marriage on the rocks, finding out the man that raised him isn't his biological father, and repressing his bisexuality, culminating in him attempting suicide when his mother died. He ended up divorcing his wife, but he managed to find an inner happiness with a balance of teaching and writing and find new love.
Beth Lestrade in Children of Time has to work very hard, up to and including dying before she can get her happy ending. Even once she marries the man she loves, she has to wait eight more years before she can reunite with him, and thenshe has to be the one to bring him back. Earn Your Happy Ending? More like... Work Your Tail Off And Is It Even Coming In The First Place?
In My Little Borg, all Earth ponies and Pegasus ponies throughout Equestria are assimilated. All the Unicorn ponies have to scrounge through the Borg's library of technology and learn how to build a fully functioning starship in under a week, in order to have any chance of saving them at all — and Twilight is the only one with access to the Borg library.
The official sequel to My Little Dashie (written by a different author) qualifies. Rainbow Dash wakes up in Equestria, only remembering her life with her human father on Earth. She acts reckless with the magic inside her and starts ripping holes in reality just to have her father back. When faced with a choice, her father leaves everything behind just to have Rainbow Dash back (as well as gaining a new friend in Pinkie Pie).
Equestrias First Human: Connor has to battle prejudice, isolation from the few friends he's made and a crazy terrorist before he can earn Ponyville's love and trust.
Princess Celestia herself decides he's earned a second one, and puts a sign on him that allows his spirit to return to Equestria, so he can have a new life, but also because of her crush on him.
Ending D of Sonic X: Dark Chaos: Tails survives the final battle and manages to cripple Dark Tails by successfully destroying the Dark Planet Egg, allowing Maledict and Jesus to depower him and seal him in Warpspace forever. Maledict and Jesus agree to a temporary ceasefire and Maledict gives Sonic his Planet Egg back. The galaxy slowly starts to rebuild and Sonic and friends return home.
The God Empress of Ponykind; after a brutal civil war that leaves thousands dead, Equestria is healing, the forces of Chaos have been driven back once again, Celestia has reunited and made peace with Horus, and there is a possibility that Luna will return to make the nation whole again.
Im Giving You A Night Call: Ed loses his boyfriend due to mistrust, the military goes after his hero persona, forced to work with his ex, forced to deal with people mistreating him due to his circumstances of his break-up, watch the woman he viewed as a grandmother get shot and killed in front of him, gets kidnapped and his automail painfully ripped off. But he manages to take down the new Homunculus gang, gets his reputation cleared and makes amends with Roy and gets back together with him.
The Wedding is Off!: Shining Armor, Twilight's friends, and Celestia become disgraced and hated due to their irresponsible actions in the failed Canterlot Wedding, particularly when they coldly turned on Twilight at the rehearsal which caused her, along with Spike and Cadence, to abandon them in anger right after the Changelings' defeat. Not only do they eventually earn the forgiveness of Twilight and everyone else upon correcting their mistakes, but Cadence rekindles her love for Shining and they have a successful wedding.
Mad World: Dib goes through a lot of dark crap over the course of this story, but in the end he's recognized as a hero, he and Zim are friends now, he's got Squee as a surrogate little brother, and he's got a friend in Nny, who's getting the mental help he needs. And the Thing in the Wall is resealed, with Zim and Dib planning to replace the Wastelocks with a sealing mechanism that won't require hosts that get driven insane by the power.
Happens in the Cuphead fan comic from DeviantArt, "Cagney Is a Carnation" by fuyuflowga. Cagney Carnation has gone through all the trouble of watching his adoptive flower children lose a casino game and get tortured by the Devil and being forced to sign his Soul Contract and offer his soul in exchange for their lives; being shunned by his peers and forced to scare them and his flower children away to have them find someone else to take care of them; losing everything he's had and almost losing his will to live; having to become a Necessarily EvilDeath Seeker in order to have the sibling protagonists Cuphead and Mugman battle him for the Soul Contract and then reluctantly killing Mugman to spur on his brother's rage (both Mugman and Cagney get better, though); and crossing the Despair Event Horizon when he tells Elder Kettle he's an irredeemable villain (before Elder Kettle snaps him out of it by telling him that the boys have the potential to fight the Devil). After all of this, however, the ending gets happier when, after the boys return in their victory over the Devil, and the inhabitants throw in a party in their honor, Cagney gets his friends and the flower children back, in which he has finally found love and his will to live again.