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 Crowning 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, 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 Luigis 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).
And now Nintendo has announced that 2013 will be the "Year of Luigi".
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.
In BlazBlue, 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 BSOD), 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.
A very minor (but memorable) character gets one in the Pokémon franchise. In Pokémon Black and White , there is a seasonal Ferris Wheel Date Moment with a Hiker-class Trainer if the Player Character is male that involves some very suggestive dialogue — but since it's Pokémon, the man is middle-aged, and the main character is a teenage boy, nothing comes of it. Pokémon Black 2 and White 2 are direct sequels that take place two years later, and if the Player Character is female, she can meet with the Hiker in the same place, where he'll mourn a lost love. In Pokémon X and Y, a worker will mention offhand that he has a Hiker friend who loves Ferris wheels, and that the man finally found love.