Perhaps it's just me, but seeing Robo in such a dilapidated state, surrounded by the fruit of centuries' worth of work makes for a session of happy tears.
Also, the fate of Schala, probably the kindest character in the game. She disappears after the fall of the Ocean Palace, and despite thousands of rumors to the contrary, is never seen in the game again, having sacrificed herself to save the others from Lavos' wrath. This troper only still has the game because he kept it in order to search every last corner of the game for Schala should one of the aforementioned rumors actually turn out to be true.
It turns From Bad to Worse in the DS version. You find Schala fusing with Lavos, her consciousness slowly being absorbed into the space parasite, and furthermore, she's become an Omnicidal Maniac as a result! And even after fighting against the new form of Lavos with all your might, all it does is piss him off and briefly snap Schala out of it long enough for her to make a really vague statement of how you can save her in Chrono Cross before teleporting you and Magus away.
What is even sadder? Schala acknowledges Magus as Janus, her little brother now an adult, for the first, only and final time by name. It's absolutely heart wrenching seeing Schala so broken that Magus cannot save her despite all the grit and will even she can see, a brother's love that is.. You really feel for him.
But possibly the absolute worst? It's arguable that the person responsible for all of this is you. In the original timeline, free of the Crono gang's meddling, they weren't present at the Ocean Palace, meaning that Schala would have used the last of her power to save herself and (possibly) Queen Zeal. Instead, since you were there, she had to use it to rescue you instead. Schala is dead or worse, the Black Omen exists and Queen Zeal is infinitely more dangerous because of you.
If all this isn't bad enough, Schala is definitely Magus's Morality Pet. She's the one person he loves and cares about and you get a glimpse of his better nature in the scene, where he begs her to fight Lavos's influence and tries to save her. He is so angry and disillusioned by his failure that he wipe out his own memory so he can start over free of power and tries to save her
This troper was HORRIFIED by the second time she encountered Magus, and she killed him her first go around. When he immediately used his last words to tell the characters how to revive Crono and died she was so upset that she immediately reset the game just to go back and change her mind on how to deal with him.
Another thing which made this troper almost cry was Magus's pet Alfador. After the fall of Zeal, the party visits the village of Earth Dwellers and Enlightened people united together. If you have Magus in your party, Alfador comes and stick to you, meowing non-stop. For him, Magus is still Janus and it also shows us their strong bond.
This troper couldn't help but feel sad at the end of the prehistoric arc. Even after spending a good chunk of game time battling the Reptites and their dinosaur cohorts, Azala's final lines about the end of the reptite era and the coming of a new ice age garners surprising amount of sympathy. The real key is Ayla (who'd been fighting the reptites long before meeting the player party) offering to fly Azala away from an impending catastrophe, resulting in this exchange:
Ayla: Come! Azala! Come!
Azala: Absolutely not! The powers that be have spoken.
Ayla: Azala... me not forget.
Azala: The future...
Ayla: What? What about future?
Azala: We... have no future...
The DS re-release slightly changed this scene, but makes the player feel for Azala even more IMO:
Ayla: Come! Azala! Come!
Azala: No! This is the will of the earth!
Ayla: Azala... Ayla not forget.
Ayla: Take? What take?
Azala: Take care… of this world.
Have people forgotten the sheer and utter hopelessness projected by Belthasar's theme, and the final (for the rest of time) "shutdown" of the robot he uploaded his brain to? Though you feel so sorry for not doing it for him...
I thought Chrono Trigger as a whole was depressing, but what really got me was the future and why it was how it was. The bad ending doesn't really help, either. It's just so hopeless... if I were more emotional I'd cry. And the thing with the plant? Probably a ray of hope that's short lived, as I view it, which would probably make the entire future even sadder for me.
Honestly! You do realize, the whole point of the bad future and the bad ending is TO MOTIVATE YOU TO BEAT THE GAME. And the only reason they had the plant in there is to imply that it will survive, and they will succeed in regrowing their own future.
Nobody's mentioned the bit where Robo has to kill his own sister in an "I Know You're In There Somewhere" battle? Granted, in the default good ending, the future in which that happened never came to pass and she's still alive, but still...
Don't forget that before that, Robo gets the snot kicked out of him by his old family members who he still considers his friends.
"Please stop. Pl...ease..."
Crono's death at the hands of Lavos, not the ending that comes after it if you don't bring him back - this troper always cries when Marle runs to Crono in the end.
In the Good Ending, Lucca doesn't want to say goodbye to Robo because she knows that, by defeating Lavos, they changed the future that Robo was born in. Therefore, Robo may cease to exist in the future. Robo tells everyone that there'll be a place for him in the future and Lucca bursts into tears.
And indeed there was a place for him. As they zip through the timestream, you see Robo and Atropos sitting on a cliff. This in itself is a tearjerker in the heartwarming way.
I prefer the Marle version actually but both are good.
Some part of this goes to the Crono's resurrection quest when most of the party except Magus had to lie to Crono's mom that he's okay when the fact is that Lavos vaporized him.
In the future, you find a small group of people clinging to life, with one woman still waiting for her husband to come back from his mission to get them some help. You soon find his rotting corpse, but with a seed that offers the slightest glimpse of hope for the rest.
Her child will constantly say funny euphemisms about her dad, which just makes it all the more sadder since the little girl will never grasp the reality of the situation until much later. The woman's own determination on raising both the plant and the child is even more tearjerking, since they both the legacies her husband left for her.
An early quest sees Frog lose his confidence, blaming himself for the kidnapping of Queen Leene. After giving Crono some kind words, he leaves the kingdom seemingly for good, and a stunned Lucca, who hates frogs, can only say "...Maybe frogs aren't so bad after all."
The songs "Epilogue To Good Friends" and "To Far Away Times" are this in musical form, or at least they bring Tears of Joy once you have gotten to know the characters so well. The first, a restating of Marle's Theme, takes the epic yet deceptively simple tune to a whole new level, since it plays when everyone is going their separate ways and may never see each other again, while the latter is a triumphant and hopeful piece that plays over either (depending on your actions) shots of Crono and Marle floating on balloons through the night sky or of Crono, Marle, and Lucca riding the Wings of Time in pursuit of his mother and cat—and seeing all their friends in every time period, showing them happy and at peace or at least doing all right. Basically, showing everything you've been fighting for the whole game, and what has now been preserved thanks to the defeat of Lavos. The last shot of the game is even an overview of the world map to emphasize what you've saved.
The scene where Lavos is falling, the song playing in the background "At the bottom of the night" really emphasizes how sad this really is, you know what's falling, you know it's bad for you and the rest of life on Earth, you seen what will do, and there's NOTHING you can do about it, all you can do is retreat into a time gate.