In "Denial" when Kent Nelson dies and then sacrifices his ascension to save Kid Flash.
According to this Ask Greg post, Aqualad's unconscious mumbling in "Bereft" translates to "Tula, please… I love you… Tula… we can still be together in Atlantis…". Note, this the episode right after Aqualad's Day in the Limelight, where he learned that Tula and Garth were together yet assured them he was truly happy for the both of them. And thanks to THIS episode's events, he didn't remember that.
"Humanity" saw Red Tornado's two 'siblings,' Red Torpedo and Red Inferno, who in their debut had come very close to outright killing the entire Young Justice team, having a change of heart upon remembering that even if they "were never human, they were heroes" by their brother, Red Tornado and joining him in stopping their new heavily upgraded 'brother' Red Volcano from all but destroying the world. For his part, Red Volcano seemed genuinely distraught that he was being betrayed and killed by those he considered his kin. His exact words: "Sister! Brothers! Stop!" were filled with genuine emotion, something he had previously never shown. All three held him down in the lava, Torpedo and Inferno being melted themselves in the process, knowing they had no other choice in stopping his planned genocide, even if they had to kill their own brother and themselves. Before Volcano died, his last words weren't swearing revenge against humanity, or condemning them for betraying him, but remorse that he had failed and they had chosen to fight against him.
Red Volcano: "Father would be... so disappointed..."]
Red Tornado's line itself is both heartwarming and heartbreaking.
The end of "Failsafe" with Miss Martian crying and the whole team traumatized.
"Disordered" has the Team talk with Black Canary in individual therapy sessions. While some of them, like Wally, who is in denial about his trauma, and Artemis, who's "too tough" to need to talk about it, others, like M'gann and Dick are more open about how they felt about the mission.
Dick is the most affected by the mission. We've gotten so used to his childish immaturity and that mischievous grin that never leaves his face, and now, seeing him so uncharacteristically quiet and depressed, it's just heartbreaking. It's even more heartbreaking when you remember that, while Dick is the most experienced member of Young Justice, he's also only 13 years old, and he's gone through enough trauma when his parents were murdered.
Dick: Hurting? Try traumatized. I finally become leader and wind up sending all my friends to their deaths. I-I know I did what I had to do, but I hated it. When we first started this team, I was desperate to be in charge. Not anymore. And-and that's not even the worst of it... Y-You can't tell Batman.
Black Canary: Nothing leaves this room.
Dick: I always wanted - expected - to-to grow up and-and become him. A-And the hero bit, I'm still all in! But that thing inside of him, the thing that-that-that drives him to sacrifice everything for the sake of his mission, that's not me. I don't want to be the Batman... anymore.
Made all the more heartbreaking when he takes up the Chains of Commanding again in Season 2 and becomes exactly what he feared. He masterminded a plot that emotionally devastated everyone around him and never once wavered in his conviction to the mission.
"Secrets" was very very dark. We find out that a guy calling himself Harm murdered his own sister to gain magical powers. In the end, it's discovered that Greta could only say the word "Secret", because "Secret" was the very last word she ever saw before she died.
In "Misplaced" when Zatanna's father sacrifices himself to be the new Dr. Fate so Nabu will release his daughter — especially poignant given she was complaining earlier how overprotective Zatara is and how much she was wishing for a little space from him.
In "Coldhearted" when Kid Flash, who was disappointed he had to race a heart on ice to a little girl awaiting it for a transplant instead of being part of the first Justice League/Young Justice team up mission, makes it with 20 minutes to spare, but is told the girl died 12 minutes before he got there. Wally spent 15 minutes fighting with Vandal Savage. Those fifteen minutes could've made all the difference, and he was wracked with guilt over having wasted that time.
And then againwhen it turns out the "she died 12 minutes ago" was a ploy by the villains. The heart does get to the right girl, and she died on the operating table, which turns out to have been a ploy by Kid Flash himself to get Count Vertigo to do the Evil Gloating thing and causes sad-to-happy Mood Whiplash.*
Artemis' break down in "Homefront" when she realizes that despite everything, the rest of the team is going to be killed, and she's going to lose the family she's made for herself. She curls into the fetal position and starts crying- it's painful to watch.
In "Image" Psimon showing M'gann her worst fears if her true form as a White Martian was revealed. All her friends rejecting her, J'onn banishing her from Earth to be alone on Mars and her very worst fear: Superboy walking away from her repulsed and saying he could never love her.
One of the biggest gut-wrench factors for that scene has to be the voice acting and how well the lines are delivered. Poor M'gann just sounds so heart broken and emotionally shattered as all of her fears are pulled out of her mind and dissected.
In "Performance", when Robin sees the "Flying Graysons" poster.
You can't help but feel sorry for Red Arrow in "Auld Acquaintance" when he finds out that he's actually a clone of the real Roy Harper and that he was programmed to infiltrate and betray the Justice League.
There's also the scene where he, paranoid, aims an arrow at Aqualad as he enters his room. After a brief Q&A to ascertain if he's the real deal, there's this line from Kaldur:
"The girl in Atlantis who broke my heart was named Tula, who is now with my best friend Garth. Meanwhile, my best friend on the surface now aims an arrow at my chest."
Season 2, "Earthlings," while engaged in a happy jaunt through the thick jungles of Rann with his adopted big sister, M'gann, Beast Boy suddenly comes to an abrupt stop, freezing stock still and gazing ahead blankly. Miss Martian tries to figure out what's going on by linking with him telepathically, and then realizes he's staring at a small lake in front of a waterfall, just as he breaks down and starts to cry. It's then we learn Queen Bee killed his mother at a similar place on Earth, and Gar was the one that found her body. For such a young kid to have his mom taken away from him so violently like that... You can't help but feel for him.
Made even worse when you remember that M'gann looked up to Marie Logan as her role model back on Mars, and thus she also lost someone very important to her. Someone please give these two a hug...
Not only that, but M'gann probably feels largely responsible for Marie's death, given that Queen Bee probably killed her in retaliation for M'gann pulling a fast one on her near the end of Season One.
Also, upon seeing the scene Gar reflexively changes from his monkey-like Shapeshifter Default Form to... himself as a boy. And you realize that he keeps himself that way because it's just easier for him to be Beast Boy than it is to be Gar Logan.
In "Alienated", we find that Kaldur has defected and joined his father, Black Manta, as his apprentice, due in part to feeling betrayed by the fact that Aquaman withheld that information from him. However, the primary reason for this shift in alliance? Tula died on a mission as Aquagirl sometime during the five year Time Skip.
Superman trying desperately to save the Kroloteans who are about to be blown up. They refuse to listen and even shoot at him. In the end, the island is destroyed and they all die, and even though Supes comes out of it pretty much unharmed, Conner understands that he still feels devastated for being unable to save the Korloteans.
We get two Tear Jerkers in "Salvage".
The first comes from Red Arrow, who has spent the timeskip searching desperately for the real Roy Harper, only for everyone who was helping him to give up because they believe original Roy to be dead. His physical condition, while still miles ahead of an average person, is much, much worse than it was five years ago. He's been reduced to fleecing money off of robbery victims to get funds, and he can barely keep himself clean. When his friends try to get him to clean up his act, he brushes them off and runs to his run down safe house. Fortunately, the last scene in the episode is happier, with his wife Chesire introducing him to their daughter Lian Harper. So I guess that makes it three tear jerkers, at least one brings out happy tears.
When Black Canary tells him that he "used to treat [his] body like a temple," his response (referring to his body as a "cheap knock-off") tells us a lot about his state of mind and why he's let himself get so run down.
How about before Cheshire introduced Lian to Roy? Jade and Roy give a subtle, but an emotional talk over Jade leaving Roy; Roy's obsession with finding Speedy lead his wife to leave him for months. Picture it: Two people who were at first enemies fall in love, and one (Jade) gives up her "evil" career to be with the hero (Roy), but one of them (Roy in this case) is so hellbent on a certain task he completely shuts out his friends and the woman he fell for.
Second, (and admittedly, not as bad as the first one) is Blue Beetle's reaction to the Golem's destruction. Once he realized that he could talk to it, he tries to get it to stop attacking a nuclear plant, and for just a moment, it looks like he's succeeding. Then an unseen villain who was watching blasts it to oblivion, destroying it. He just sits there for a moment, stunned by what happened and filled with grief.
And before that, Superboy saying "I can relate" when he hears the Golem's death wish. He's been where the Golem is, thinking of himself as an unnatural existence.
In The Stinger to "Bloodlines," Bart's annoyed "Well, better get in character."
To go into more detail: The personality Bart's shown the entire episode is a facade used to hide the fact that he's come back in time to stop a Bad Future. He knows that it's a one-way trip, and he doesn't care. And finally, saving the Flash's life wasn't enough to change the future, and all he did was cure his friend - the episode's villian - forty years ahead of schedule.
Pretty much, you'll laugh your ass off at all of Bart's antics. Then, you watch it again and the dread slowly starts creeping up on you.
In "Depths", viewers learn why Conner and M'gann broke up. Alone in the bioship they discuss that it was because Conner was alarmed of M'gann telepathically interrogating villains leaving them vegetables. She shows absolutely no remorse and claims that the ends justified the means. Conner thinks she's become no better than Psimon. M'gann gets very defensive and asked why didn't he tell Nightwing or Martian Manhunter about it. Connor had hoped he'd matter enough for her to stop. The final straw was her telepathically wiping his memories so he wouldn't be upset at her. He did find out and felt betrayed. Conner: "After all we've been through how could you think I wouldn't recognize your touch inside my mind? Didn't you know what that touch meant to me? And to have you pervert it like that..." Conner's voice when he says that and M'gann's eyes filling with tears is heartbreaking.
Then there's Nightwing looking at the picture he took of himself and Artemis on her first day of school, right before he tells Wally about her "death". If the line "We'll laugh about this some day." doesn't make you tear up, nothing will.
And before that there's Artemis getting "killed" by Kaldur'ahm and Nightwing using cpr and trying to revive her. And Superboy coming up and saying he cant hear her heartbeat. And then the scene switches The Team all crying in mourning. With M'gann the most hit and Superboy wanting to comfort her but can'tnote Her boyfriend was also captured.
It turned out Artemis didn't die and Aqualad didn't betray the team. But one can't help but feel once the ruse is discovered, it would destroy the team's trust.
Halfway between Fridge Horror and Tear Jerker: Zatanna has grown to womanhood and joined the Justice League. Dr. Fate, who does not seem to have relinquished his hold on her father, is still on the team. For all intents and purposes, her father died when she was 14 and now she's on a team with the "man" who killed him.
In "Satisfaction" there was a plethora of these:
Artemis Lian Crock. As revealed on her tombstone.
When Artemis's Mother is at her grave and tells Wally how hard it was and she needed him to get through it, he couldn't even look at her out of guilt for lying. Even her father and sister were there, swearing revenge on Aqualad and Black Manta for one reason or another.
There is a memorial hall to fallen heroes: Ted Kord, Tula, Artemis... and Jason Todd as Robin.
After going down with several others to visit Artemis's memorial, Tim can be seen in the background lingering at Jason's. He never knew the last Robin personally but he still pays his respects.
Practically EVERYONE is now hunting Aqualad down, while we know his loyalties lie, it is heartbreaking to see the results of his actions.
Only two people remembered Superboy's birthday and only one of them was a member of The Team. It's even worse, out of the two, the one who wishes Conner a happy birthday isn't even aware that he's Superboy.
Green Arrow absolutely hating himself, thinking he's the worst mentor ever, having led the original Roy to be kidnapped and captured for nine years, letting the clone Roy rebel, eventually neglecting his health and wallowing in self-pity, and having Artemis killed (her death was faked, but he doesn't know that). Your heart goes out to him, knowing he can't really be blamed for any of that. Especially the last one.
In "Darkest", Beast Boy is watching episodes of "Hello Megan," so he can see his dead mother again.
Before Aqualad blows up Mount Justice, the viewer sees Artemis not as the evil Tigress but as the original, blonde Artemis, as she asks him, in a sad voice "are you sure you want to do this?" Quite poignant.
After the explosion, Wally storms into the Hall of Justice to confront Nightwing, as he questions whether Aqualad is really "acting" to keep up his cover or is actually a triple agent. These two friends, who had each other's back through thick and thin, who knew each others' secrets - they're now at each other's throats.
Worse, according to this Ask Greg post, the only reason why Wally knows about the plan in the first place is because Artemis insisted that he was let in on it or she wouldn't participate. Meaning that Nightwing was willing to let his best friend believe that his girlfriend was killed. The ramifications between them after the reveal would've been worse than the one above.
Seeing Nightwing making so many sacrifices for what he believes to be the greater good... just like Batman, which is what Bruce was trying to avoid in the first place. One wrong step, and all his effort will have been for nothing.
Consider the likeliness that not even the League knows about this plan (Green Arrow sure doesn't, as he thinks Artemis is really dead). What do you think would happen when or if Bruce gets back from that trial and finds out about the plan, with all of the extremes Dick has to go to just to try and find out who the partner of the Light is?
Making this even sadder is his therapy session back in season one, explicitly stating "that's not me" about such mentality. Either the original statement was a complete (yet convincing) ruse, it's a case of Aesop Amnesia, or he's full of self-loathing and inner conflict because of this charade that he perpetuates on a daily basis.
Bart Allen seeing Mount Justice blow up. He's been stuck in the past with his solace being that he made something better, and then he sees things happen the way they were before and knows he hasn't been able to stop it. Made worse by the fact that he brought the tech into the cave, so this could be considered his fault.
In "Before the Dawn", M'gann's Heroic B.S.O.D. when she discovers Aqualad was Good All Along...only after she Mind Raped him into catatonia. Not to mention the way that Conner was looking at her at the end, knowing full well that she must've done. He had warned her about doing that so many times and in the end he was right.
Artemis: M'gann, what have you done?
And to make it worse, we see all of his memories, including one where he's standing where Tula's marker in the memorial stands — making the very pact with Nightwing that led to this.
Actually the worst part is he was resisting, so she doubled down. Then, while he was on his knees she finished him off. Given that it took Psimon five years to recover and he was a vegetable when Artemis got to him. At best, he'll need Psimon or J'onn to help onto his feet, and if the former does it, there goes the whole thing to the bad guys.
Watching Black Beetle smash Cassie into the wall savagely and repeatedly while flashing to each team member he had beaten unconscious was very draining, emotionally. He may be the most powerful and terrifying thing the team has faced at this point.
Why was Impulse hanging out with Blue Beetle the previous episode? Because as he puts it, Blue Beetle becomes the "biggest baddest Big Bad of all time". He wants to prevent Jaime from ever becoming that monster.
Jaime's fear of the Scarab throughout "True Colors", the look on his face when the Atom and Bumblebee can't remove it, not wanting to go on the mission from fear of the scarab taking over and bringing on the apocalypse.
Robin: Blue, what gives? Last time you threw down with this guy you were hardcore!
Blue Beetle: That wasn't me; Scarab was in control.
Arsenal and Scarab: So give it/me control again.
Blue Beetle: Trust me, I'd like nothing better, but I can't risk that, not with Impulse's prophecy hanging over my head.
And to make matters worse it became a Self-Fulfilling Prophecy because he was so eager to get rid of it and trusted Green Beetle, who he only met a day or two ago. Now he's trapped in his own body and under the Scarab's control.
Aqualad's mindscape in "The Fix" is Atlantis in complete ruin and him mumbling and whispering to himself both in Atlantean and English about what is left of him and his loneliness after M'gann's Mind Rape, going to the point that he has no face. He didn't deserve that at all.
What makes it worse is that he's not the one attacking Artemis and M'gann—it's Tula, the girl Aqualad loves and who died during the Time Skip, protecting what's left of him.
And later, As Aqualad's mind is slowly being repaired, in the real world, Black Manta comes to check up on the process and we hear Aqualad speak his first word in a long time: "Father." Manta immediately rests by his son's bedside to reassure that he's truly there. For that one moment, you forget that he's an evil villain working for The Light and realize that he's still a father.
Poor La'gaan, his girlfriend has been avoiding him recently and not returning his calls, plus she did go talk to her ex what was going on, but not him, her boyfriend. It's obvious La'gaan is very insecure and all of this is happening right after all that time being stuck as one of the Reach's prisoners. Even those who said they don't like La'gaan, did genuinely start to feel pity for the fish boy. The broken expression on his face as he's pleading her to tell him what's going on, and his voice even cracks when he says "please." Then to top it off, Deathstoke and Tigress attack, kidnapping his girlfriend, with La'gaan being knocked out and having his leg broken. As such, he throws a fit when he wakes up, feeling like he failed to protect his girlfriend. Furthermore, immediately afterwards, he learns that his rage against Aqualad and his mourning of Artemis were all misplaced and the result of his leader's deception. Poor guy just can't catch a break.
Tye, after being kidnapped, tortured and experimented on, gets to see his best friend not acting like himself, having been put on mode and turned into an agent of the Reach. Oh, and apparently being willing to sacrifice Tye and his three friends for victory. Tye's face when he realizes that Jaime's not the same is heartbreaking.
There's something very tragic about Arsenal panicking and spacing and when that doesn't work abandoning his teammates after Blue Beetle turns on them in "War". Remember that this is the guy who's had his arm chopped off and has been kept in ice for eight years. What he says right before opening the airlock really shows how traumatized he still is by that incident.
In that same fight, Superboy questioning Blue Beetle's betrayal and the look on his face before being knocked out is heart-breaking.
There is a belief that parents, by some combination of love and having known them their entire lives, are nearly always capable of recognizing their children. When Miss Martian brings Sportsmaster and Cheshire into Artemis' mind to prove that she's alive, Cheshire believes because she loves her sister and recognizes her presence. Sportsmaster isn't convinced until Artemis uses a fighting move that he taught her. Sportsmaster is such a terrible parent that he can only relate to the daughter he raised in the context of fighting. He neither knows her nor cares about her beyond that. Artemis is painfully aware of the fact.
Artemis: "Yeah. So glad it turned out you're not dead, baby girl."
Nightwing holed up in HQ as the last member of the team. Especially since he's holding Robin's birdarang, and probably flashing back to the last Robin he failed to protect.
It's hard watching Black Manta showing such care and devotion for his son when you know sooner or later he'll find out where Kaldur's true loyalties lie. Making it worse is the way that (from Manta's point of view) Kaldur was finally able to recover from his partial catatonia was by seeing his father in mortal danger. Manta believes this completely.
As of "The Hunt", literally everything about the "runaways" is heartbreaking. First the Reach kidnap them from the streets and in Virgil's case from home, then from their point of view they are betrayed by Blue Beetle, and just when they think they found someone they can trust in Luthor they find out that he lied to them too. These are kids that are probably going to be chased down by everyone in the series from the League all the way to the Reach and they have been betrayed and lied to by so many people they likely won't be able to trust anyone at all, so when someone tries to sincerely help them they probably wont trust them either out of fear of being lied to. These kids literally have no one to turn to and they are all on their own.
Arsenal getting kicked off the team also counts. The guy just can't catch a break, can he?
The breakup of Miss Martian and Lagoon Boy. From the moment you hear M'gann say "We need to talk", you know things are about to go down, and since both of them had received Woobie points recently, it doesn't make what happens any easier.
Then later when M'gann wants to talk to Conner, she finds out that he's going out with Wendy Harris and is hurt.
Jaime begging for his teammates' lives. The fact that it was his body that was going to do it, and the panic in his voice was just gut-wrenching.
Black Manta learns of his son's betrayal, and is honestly crushed. He goes nuts when Aqualad attacks him, saying he will teach him the ruthlessness he needs to survive if he has to beat it into Kaldur's skull. At the end, the rest of the Team is congratulating Kaldur on a gambit well played and he just looks back at his father's unconscious body.
The episode takes place on June 19, 2016. Father's Day.
Oh god the final episode, Wally West DIES.
Barry realizing that Wally is taking the brunt of the excess energy, and calls out for Bart to slow down so they can siphon off some. He reaches out to grab Wally, and his hand goes right through him. That's when Barry, Bart, and the audience realize it's hopeless.
Barry tries to comfort Artemis by telling her that Wally loved her. She just bursts into tears and collapses onto the ground. M'gann immediately rushes in to embrace her while everyone else just stands silently.
The wordless scene where Artemis goes to Wally's parents' house with tears in her eyes and they hug.
And afterwards, Bart and Artemis's new looks.
Nightwing quits the team because of his depression over losing his best friend.
It's pretty minor, but after Black Beetle confirms that Green's Scarab was on their side, he destroys it, and you can hear it scream.
This probably is as much a Heartwarming Moment as it is a Tear Jerker: Wally, with his scientific genius, knew going to help Bart and Barry siphon off the energy would be suicide with his slower speed. So he zetas right to Earth, no quips, no "Eureka!" moment, not even a good-bye or a last kiss to Artemis. That's the sad part. The heartwarming aspect? He did so so that Artemis's last vivid memory of him would be Wally kissing her in Paris underneath the Eiffel Tower.