What better to start this page than with the Eight Melodies?
The first Mother game does this with its Final Boss, too. Giegue is defeated by a song his adoptive mother Maria sang to him when he was an infant. He tries to stop Ninten, Ana, and Loid from finishing, but fails and instead flees in confusion (though not before promising Ninten he'd come back.) It was incredible, and quite touching too.
How about the cute Toy Ship moment between Ninten and Ana that Teddy allows out of the blue close to the end of the game? It's primitive 8-Bit RPG dancing, but it just begs you to go "D'awwww..."
EarthBound. To defeat the very final boss, a Cosmic Horror, you can't just smash him with your attacks. You eventually have to use the oft-useless pray command to cause people you've helped over the game stop for just a second, wherever they are, and hope you are OK and that you are well wherever you are. Heartwarming. After a few attempts the game runs out of these people so The Chick uses the turn to just cry out into the darkness of time for someone, anyone to help them fight this horrible being. The very last person to wish them will and give them the power to defeat the horror, you. The game actually asks you to pray for them to be able to defeat the final boss and if you were under a certain age, or a certain level of naivety, or simply surprised at the No Fourth Wall moment of it all, you prayed for them.
That's when you realize why the game asked you for your name, which was a good ten to twenty gameplay hours ago if you're speedy. If you don't remember the game asking you for your name, it's even more awesome.
And in case that isn't enough to tug your heartstrings, the ending - both when Ness walks Paula home and the ending credit roll - have two of the most moving musical pieces in video game history.
The memories that flash in your mind as you visit the My Sanctuaries. The image of being held by both your parents as a baby, hearing her prayers that you grow to be a strong young man.
In Earthbound, when you return from the final battle, especially when Poo told the gang that their adventure was over and performed "PSI Farewell". Also to be included that they all have to part and go back to being "regular kids".
In the same scene, Jeff tells Paula and Ness that, should they ever get hitched, he could be "the guy who helps fix their electrical appliances or something." To make it even better, you see his sprite walk up to both of them and makes a little shuffling motion. It's simple, given his sprite's limitations, but it's unmistakably a hug. Jeff, you were such a sweet guy...
Ness escorting Paula home at the end. Especially since it's implied that Paula was trying to confess her love for Ness. Just listen to the background music.
When Paula asks Ness to escort her home, you can say No. If you do, Paula decides to escort him home. When you arrive, Ness' mom teases him about his girlfriend, and Paula joins Ness' family for the final in game shot.
This kind of counts for Fridge Brilliance as well: if Giygas rules in the the future that means that the Chosen Four failed some time during their adventure, probably Giygas. Why? Because they didn't have YOU to pray for them. Meaning YOU saved the Earth, and possibly the whole universe.
In Dusty Dunes Desert, you can find two very small, almost completely unnoticeable sesame seeds. Both of them will mention the other and refer to him or her as a long lost love. It's easy to dismiss this as just another weird thing the game throws at you, Until...
Ness getting homesick if he doesn't phone his mom in a while. It's a very small detail that makes this game even more lovable.
The second row of credits where the game's main theme (and the sound stone's music) Smiles and Tears plays while all the photos the photo man took that you bothered to look for are shown while the developer's names scroll, its just such a nice way to look at those pictures and be reminded of all the things you did in the game after beating it and Smiles and Tears just makes it a really long sweet moment (especially the part where it says I miss you) and the credits end by thanking you the player acknowledging you one last time before the credits end.
Itoi confirmed on Miiverse that Mother 2 will be on the US and EuropeanWii U Virtual Console.
The ending. Especially during the credits when the Masked Man reverts to Claus and runs off with Lucas. Or when it shows Hinawa releasing the pigeon. Or the new logo with the completely wooden letters and a normal Earth. Or, well, EVERYTHING.
At the end of Chapter 4, in which DCMC plays one last concert for their buddy Lucky AKA Duster. And then there's the flashbacks of their times together as a band... How Lucky learned to play bass... How they all stuck up for one another... *sniff* Now THERE'S True Companions for you!
Hey, big guy in the sky, look out for our pal...
Bit of a Harsher in Hindsight example, but it deserves to be mentioned. In Chapter 1, Flint spends a good part of at least several in-game hours trying to find his family, after they never came back from the burning forest. After finally finding them, the reunion he shares with his boys is very sweet.
Not to mention every single member of Tazmily villiage pitches in to help, since in Tazmily, everybody cares about everybody else. That's heartwarming and retroactively sad in and of itself.
The little speech the last save frog gave you for playing through to the end is one, at least for me...
"I am the final frog in the game. It's been such a short time, but it feels long, too. In any case, thank you for your continued patronage through it all. For me, and all the other frogs, I thank you. * hop* *teardrop*
The last Duel / Puzzle Boss fight against The Masked Man aka Claus. Hinawa keeps talking to Claus to try and make him remember who he is, and Lucas refuses to attack for most of the battle (and doing so is fruitless once you can attack). All you can do is guard, heal, and pray. At the end, Claus wakes up... and kills himself. But he and Lucas embrace at the very end.
Claus: I'm sorry it turned out like this. I'm really happy you could be with me just before the end... Thanks. Dad. I'm sorry I didn't listen to you. I'm going to where Mom is now.
Immediately following this scene, Flint asks you to forgive Claus for being "hasty". After Claus strikes him down twice, he just gets up (which might qualify as a CMoA), and asks you to forgive him. Now that's a loving father.
After Lucas pulls the final needle, and the world is shown being destroyed as the Dragon awakens, it cuts to a completely black screen with just the word 'END?' in the center. The trick is, though, that you can walk away. As you do so, though you cannot see anything, you find that you, as in the player, are in the game and are talking to the characters. They all reassure you that the world has been recreated and that they couldn't have done it without you. They all direct you to Lucas. Once you encounter Lucas, he as well thanks you for helping him. He wishes he could talk to you longer, but knows you have to leave. But as he gives you his goodbyes, he asks you what your world is like. He asks you if your world's going to be okay. He... he tells the world to be good to you like you were good to his world. And then they credit you, the player, in the ending scroll!
Porky doing the same thing during his fight might count, too... He's probably addressing not Lucas, but you, the player, thanking you for playing to the end. How many games have the final boss thank you for playing the game to the end?
There is the moment you find the Real Bat. This might sound corny, it feels like Ness was right there with Lucas, lending him strength.
...later, when you get to the boat ride in the Empire Porky Building, the final exhibit is the two sesames, together at last. Awwwww... even plant life can find love in this world.
How about the ending title screen It's minor but there's just something sweet about seeing the title screen go from a metallic sphere with wood covered in metal to seeing it become planet Earth with now full wooden letters around it and the word end the music that plays during the screen is pretty good too.