The Eight Melodies. No matter how it's covered, be it 8-bit, rock, or orchestral, it expertly conveys the sense of childhood adventure. It subtly invokes fear, innocence, heartbreak, and hope, all at once. There's a reason so many professional covers exist.
The idea of the Eight Melodies in the game in general. Think about it; A childhood antique doll that used to be played a ton of times, a mother and a child bird separated by humans who didn't know any better, a monkey who's caged and locked up in a zoo, a dusty old piano that plays on its own, a lone cactus in an empty desert where a war happened and exterminated the rest of its friends, a dragon whose been sleeping away its life, a robot companion who defends you from everything, and lastly, the tombstone of your dead and loving great-grandfather who built the robot companion knowing that you might need it someday.
Try reading the above in one go without getting tears in your eyes.
Queen Mary's final scene. Her story in general is tearjerking.
"Oh! Giegue! I loved him... I loved him, as if he was my own child... He was always wagging his tail... just like a pup..."
Teddy's fate at the hands of R7038. He gets better. (at least in the English prototype and the GBA remake)
Ness' Eight Melodies are also very touching, especially when you listen to it from the simple music of the Sound Stone.
When Jeff meets his dad. Nothing really happens. Jeff meets his dad for the first time in ten years, his dad does nothing but offer him a donut and help him continue, yet he clearly wants to see his son, and yet he knows it wouldn't be really able to keep him happy. Poor Jeff. Poor Dr. Andonuts.
Paula praying to friends and families during the final battle against Giygas.
Paula prayed from the bottom of her heart.
"Please, give us strength... if it is possible... Please..."
"Somebody help us..."
Paula's call was absorbed by the darkness.
Giygas's cries of pain from a mind so utterly broken, alone and lost in a void he doesn't even understand are heart wrenching. All he wanted was a friend, and all he was was scared.
"I'm so sad, Ness..."
This 8 Melodies video sums up the two above examples of just how tragic a character Giygas really is.
Take his appearence and backstory from MOTHER 1 into account. The entire series happened because of the horrifying choice Giygas was forced to make: his race or his parental figures' race and family. Giygas's rational mind, which was perfectly seen in Mother 1 when he called off the attack because of the love he felt for Maria, is completely gone because of the trauma he recieved and the evil power he absorbed.
The ending credits song "Smiles and Tears'' from when you've beaten the game.
This is especially a tear jerker when you realize that you'll never see the four characters that you've grown to love again.
All the zombies getting trapped in the circus tent in Threed is gut-wrenching when you talk to the people around the tent afterwards.
Arguably, MOTHER 3 in general — starting with Hinawa's death and Flint's subsequent breakdown in Chapter 1, the entirety of Chapter 6 where Lucas chases his mother's ghost through a field of sunflowers. This game wasn't tagged "strange, funny and heartrending" for nothing, you know.
The final boss fight was probably the biggest example here. You find out that the Masked Man is Claus, your brother who you haven't seen in three years. Then when he tries to use PK Love Omega, Flint jumps in front of Lucas to save him. Then when Lucas is about to give up, Hinawa's ghost comes back and convinces them to stop fighting. We see a flashback to when Lucas and Claus were babies and Hinawa was still alive. After realizing who he is, Claus kills himself to be with his mother. It also doesn't help the Love Theme is playing the whole time, which is a sad song on it's own.
"Claus... Claus... Claus... Come to your mother... You must be so exhausted... Come here, Claus."
There is a long, straight hallway towards the end of the game, featuring nothing but a tile floor, a red carpet, and this music.
The abuse Salsa endures can be very tear-jerking to animal lovers. To the extent that the player can have him examine a mirror, and the flavor text prompted will be "What does a smile look like again?".
Realizing Fassad was Locria, the seventh Magypsy. On one of the floors in the Empire Porky Building, there is a Magypsy's shell house. Inside there are crates and presents of bananas, banana peels litter the floor, a Magypsy's memento (a Razor and Lipstick) that can come in handy as with the other mementos, familiar looking horns on the table, and a Magypsy's bed, where laid out on it is Fassad's clothing. Finally, when you reach the entrance of the next elevator, there is a lone mouse. What he says will make you can't help but feel sorry for Porky's first lackey throughout half the game.
"I don't think Locria is coming back anymore. Oh, me? I'm a mouse Locria liked to dote over. He had a creepy "Nwehehehehe" laugh, so he might've seemed like a mean person in most people's eyes, but he was very nice to me at least. Do you think he'll be coming home soon? I'm so lonely."
In EarthBound, two sesame seeds- one white, one black- can be found in desert. They're each only one pixel big, and if you talk to them, they'll ask you to help them find each-other, because they're in love. The sesame seeds cannot be interacted with beyond this, and they're on completely opposite sides of the desert. Twelve years later, Mother 3 came out. In the last chapter of the game, you can find a single black pixel and a single white pixel sitting on a stand, side-by-side.
The end of Chapter 4, in which DCMC bid farewell to Lucky, aka Duster.
Claus: Everyone's here, Lucas. Everyone's waiting to spit on you, throw rocks at you, and make your life hell. Who's "Everyone"? ... Everyone you love.
The movie theater. It's not just that Porky wants to show off Ness's adventures in his movie theater. It's that he had to have actually taken the time and effort to have them properly filmed.
The DCMC concert at the Empire Porky Building. Knowing that the world might end, they decide to hold one last concert to rally everyone's hopes.
Leder's Info Dump. When you come upon the realization that you're essentially on untouched utopia, created so the lives on it were to be the happiest, truly perfect ones- and it was all corrupted in a moment by Porky and his happy boxes? Bring on the crippling depression and a virtually nonexistent will to go on. Until you realize you do have something to fight for- a reset button. Or, at least, what might be a reset button, if Masked Man isn't truly corrupt.
Reggie's quote- "We can forget happy things. We can probably forget sad things too. People have the power to forget." The people of Tazmily had all forgotten their previous lives, driven to destruction by society and technology. They exist on a perfect place of harmony and happiness. Claus had forgotten who he was, forced or not. Porky has forgotten kindness and love, and Flint refused to accept his wife's sacrifice. Lucas seemed to be stuck in this stagnant form of grieving for the entire game, never dwindling on his happy memories. It's especially apparent when he looks into the mirror later in the game, the one he looked into in the beginning. Hinawa's reminders to Lucas become all the more powerful, along with the Magypsies' messages. Tazmily Village quickly forgot their peaceful ways to usher in a newer, modern age, completely accepting it and transforming Tazmily, even going so far as to shove the elderly into a decrepit home and abandon their hometown for the city. People have the power to forget. To move on. And it's not always, necessarily, for the better.
The ending after the Dragon is raised and we watch the world destroyed, the player gets to walk around as, presumably, themselves, listening to the people of the MOTHER 3 world thanking YOU, the player, for all your help, and asking you how you are doing in your world, or if the world you are in is treating you well.
"Hey world, treat our friend well!"
We could flood the page with links, but instead, we'll just put it simply: This game's utterly magnificent soundtrack is a huge reason as to why it's so sad.