Johnny Sasaki of Metal Gear finally gets some luck in Guns of the Patriots. He gets cured of his bowel problems, stars in his own Moment of Awesome, and then marries his commanding officer/long-time crush Meryl in the ending of the game.
After all the abuse he suffers through in Disgaea 3, Almaz ends up getting what he wants. He marries Sapphire in the post credits epilogue of the normal ending.
In the normal ending of Disgaea 2, Butt-MonkeyGoldfish Poop Gang Axel gets something as well. he regains his reputation as the Dark Hero by making the entire Netherworld think the Overlord Zenon thing was just him trolling them.
Luigi of Super Mario Bros., Nintendo's poster boy for Butt-Monkey, got thrown a bone by Super Smash Bros. Brawl. He ends up as one of the four characters who save the rest of the heroes of the overworld. Granted, it's after a scene where he's scared of Waddle Dees and gets sneak-attacked by Dedede, but the clumsy little plumber helps Dedede save everyone.
There's also Luigi's Mansion, where Luigi finally takes a starring role, and saves Mario, despite being scared out of his wits (this is technically the second time this had happened, but nobody counts Mario Is Missing!).
In Mario & Luigi: Bowser's Inside Story, Bowser saves the Mushroom Kingdom from the Dark Star and Fawful, only to end up getting beat up by the Mario Brothers once again after challenging them. After the credits, while he's recovering from the injuries, he gets a present from Peach and the Mario Bros. It's a Mario 64-like cake with his face.
Xenosaga, Allen ends up with his crush, Shion; and the person she cares about more than him has to leave until some reincarnation in the future.
That person gets her bone in Project X Zone when she finally finds Lost Jerusalem.
Noel Vermillion has nothing but sad endings. Except that one ending involving her getting enchanted with Litchi Faye Ling's cute panda hairpin and pins on it happily. It's the closest thing to 'happy ending' she can get. The true endings also improve things for her somewhat (although the second game is still somewhat bittersweet despite the fact that she's been convinced she's a person despite her Artificial Human status and never having been in the timeline before and hanging around with her best friend since her other best friend has undergone a Heel–Face Turn and wants to kill her.
The gag ending for Lambda-11 looks like this when she gets a pet insect and makes friends with Makoto but this turns into a Yank the Dog's Chain when Kokonoe unknowingly throws the unfortunate creature away and erases L-11's memory of the diversion (made even worse by the fact that had she known Lambda wasn't an Empty Shell she may well have been much nicer (or as nice as she is to Tager).
Throughout the Chronophantasma story mode, Litchi is forced to eventually pay the consequence of her turn to NOL, being pitted against Bang and breaking his heart and assisting Relius in a plan for world destruction for the sake of Lotte's existence, all with her grief untamed. But by the end of it, not only Bang indirectly freed her from Relius' influence (by wrecking his plan so hard he fell into Villainous B.S.O.D.), Litchi is currently with Carl, a boy that cared for her (and she cares for him too) and more capable to ease her grief and maybe make her give up her destructive Tragic Dream, the cause of all of her suffering.
In the ending of Ace Attorney: Trials and Tribulations, after two games of being verbally abused, whipped, having his pay cut to unbelievable levels, had a tracking device placed on him and then fired (though he gets rehired), it's implied that Dick Gumshoe finally hooks up with his longtime crush Maggey Byrde.
In Case 1-3, there is a fantastic moment where Edgeworth not only stops Dee Vasquez from ending the cross examination, but points out a vital contradiction in her testimony, thus giving Phoenix what he needs to prove her guilt. Given how Edgeworth has done nothing but make the cross examinations miserable for Wright (all while being smug and condescending), this is very welcome.
At the end of Investigations 2, Edgeworth actually raises Gumshoe's salary for a change.
As a Meta example, Raichu was considered The Artifact as soon as Pikachu became a Breakout Character, with Pikachu getting all kinds of event-exclusive moves, formes, and playing a major role in most Pokémon media. Raichu, by contrast, got nothing new added to it, only shows up once every so often in the anime, and is almost never marketed anymore, to the point the fandom started joking Game Freak wanted people to forget it even existed. Then Pokémon Sun and Moon happened, however, and Raichu was amongst the various Pokémon to receive an Alolan Forme.
In Kratos'Mortal Kombat 9 ending he is personally thanked by Raiden, the only god to not stab him in the back or treat him like a tool.
Reptile, meanwhile, is finally given a break in X after multiple games featured him getting screwed over by his masters. His new boss, Kotal Khan, is a Noble Demon who values and greatly respects Reptile for his loyalty and sense of duty.
Pierce Washington of the Saints Row series usually plays Butt-Monkey to the other Saints, with the Boss constantly disregarding his overly complex plans in favour of the much quicker (and much more fun) method of just barging in and shooting everybody between him/her and his/her objective. In Saints Row IV, his loyalty mission involves the Boss actually letting him do one of his plans for once.
Agents of Mayhem takes place in the Alternate Timeline created by Saints Row: Gat Out of Hell's Cosmic Retcon ending. In this timeline, the Saints do not exist and therefore the man/woman who would become the Boss never got involved in crime. Instead, Pierce is known as "Kingpin", and is the equivalent of both the Boss and Benjamin King. After succeeding King as leader of the Vice Kings, Pierce united the Vice Kings, Westside Rollers, and Los Carnales under one banner through peaceful negotiations.
Waver Velvet of Fate/Zero became "Lord El-Melloi II" after the Fourth Holy Grail War but all he ever wanted was to be with his King again. It's stated to be a Tragic Dream in the written midquel series, the Lord El-Melloi II Case Files. He gets his wish by becoming a Servant in Fate/Grand Order.