This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Batman Beyond
In the pilot "Rebirth," after much silence, Terry finally breaks down after his father's death.
It's even more heartbreaking when you realize that the last thing they did was fight.
Terry:[tears in his eyes] I yelled at him, Mom. He grounded me, and I wouldn't listen. The things I said... [his mom hugs him] I'm such a jerk...
Bruce Wayne's last fight as Batman in the same episode. The fact that Wayne struggles to keep up with the goons and gets a heart attack at the worst possible time, forcing him to pick up a gun just to save himself and the child of Veronica Vreeland, one of his few remaining friends from BTAS. You can honestly understand why he retired after that.
Spellbinder's last two victims before he targeted Terry in "Spellbound". First, poor Deakins is hit and he drags a valuable dress around, thinking he's in the middle of a war and dragging a wounded comrade to safety. Especially not funny for anyone who knows anything about PTSD. Then he goes after some poor woman, on her wedding day. Scaring her out of her mind and nearly getting her killed at least twice.
"Meltdown": Freeze's swan song episode.
His last words: "Believe me. You're the only one who cares." No, he's not, Freeze. He's not.
Terry's utterly heartbroken "Oh, Fries..." when it became apparent that Victor returned to his old ways. Mostly because, as the above quote says, Terry was the only one who had any faith in him.
The climax of "Dead Man's Hand" where Melanie's father orders her to come save him just as a security guard shows up. Terry whispers: "Don't do it. Just go" with the most heartbreaking voice and facial expression. The scene of him watching the police take her away is also just as devastating because just as she's in the back of the truck, Melanie sees Terry in the crowd.
Near the end of the episode, when Ten is shot at and starts to fall, Batman catches her as she looks at him remorsefully, saying, "I don't suppose I could convince you to let me go." We're then treated to a somber Kubrick Stare from Batman, which says a lot with only one expression, seen here◊.
"Earth Mover" is riddled with heartache. You have a man buried alive in radioactive waste seeking vengeance on his business partner who raised his daughter in light of the accident. He gets a Heel–Face Turn when he uses the last bits of his life to allow them to escape with a heart-wrenched "Jackie."
The kids who fell victim to Spellbinder's VR chambers in "Hooked Up". Especially the sweet innocent girl Jessie. Unlike Donny, whose fantasy was rather predictable for a kid his age. Jessie's "perfect" life seems almost ordinary by comparison. The one thing that would make her most happy? Working at a fast food restaurant, where her manager (a rather geeky-looking but adorable guy named Wendell) asked her to marry him.
Max's fantasy is just as innocent, her whole family was together (instead of her parents being divorced and absent) and were all praising her and going out of there way to make time for her.
"Out of the Past"
The final line:
Bruce: Rest well, beloved.
Earlier in the episode, Bruce looks over some pictures of his more notable relationships. It's sad because he realizes how much time has gone by and just how alone he is.
"Disappearing Inque." Bruce has donned the exosuit to save Terry from Inque. Terry looks on in shock and terror, especially the scene where Terry screams a Big "NO!" after Inque punches Bruce across the room. The exosuit puts such a strain on Bruce that he could very well die.
Made even more heartbreaking when you stop and think about what happened the last time Bruce's protege was kidnapped by a dangerous supervillain, as revealed in Return of the Joker. Tim Drake ended up severely messed up because Bruce let him fight crime on the streets, and swore off ever allowing another young partner to do the same. He lets Terry don the Batsuit, and Terry is kidnapped and hauled off someplace Bruce can't identify? Bruce must have been kicking himself over that one...
Ace's backstory in "Ace in the Hole," and Bruce's efforts to keep up appearances while he's missing.
Bruce: Don't worry, boy. I won't ever let anyone hurt you ever again.
The part of "Revenant" where Matt says he wants to hold a seance because he doesn't want to forget his dad. Terry and Mary exchange a look of despair, and ultimately Mary has to say that ghosts aren't real.
"Mind Games", a lost girl named Tamara frantically calls Terry for help. He's forced to use every ounce of his (and Bruce's) detective abilities to find Tamara and every ounce of his combat abilities to fight the super-psykers who abducted her, all while comforting her to the best of his ability.
In that same episode, Terry and Bruce flip through pictures of missing children to see if Terry recognizes one of them. Many pictures appear onscreen, only of young girls. Terry is obviously shaken by it.
However since Terry probably told Bruce that he was being 'haunted' by a young girl Bruce probably narrowed the search down to ONLY young girls. Terry's just shaken by how MANY there are, and that's just one group.
Try to think of a moment in "The Last Resort" that isn't depressing in some way or another.
Such as Sean Miller's Redemption Rejection at the end of the episode after helping to liberate his wrongly treated inmates.
Or when Chelsea describes what "ISO" is; total sensory deprivation (no light, no sound, no company, nothing) and when she starts to describe its effects on her, her voice cracks, the tears start, and all she can do is beg Terry to get her out of there. Seeing the bubbly Chelsea reduced to this is shocking as well as heartbreaking, and makes her refusal to immediately forgive her father for sending her there much more understandable.
"Betrayal." The whole episode is pretty depressing with Terry feeling responsible for his old friend Charlie turning into the mutant "Big Time" and returning to a life of crime. Terry tries to convince Charlie to leave his gang and turn himself into the cops; it looks like he's finally gotten through to him, but when the gang gets taken down by the police, Charlie reveals that he had no intention of turning himself in or getting cured, and he was only using Terry to get rid of the gang so he could start his own criminal empire. Then to top it off, he tries to kill Terry in spite of everything he's done to try and help him and, after a fight on the bridge, Charlie ends up falling to his death and Terry just stares sadly and Bruce tries to comfort him over it and relates his own fallout with Dick Grayson and/or Harvey Dent becoming Two-Face.
Bruce: I'm sorry. I know how hard it is to go against a friend.
Terry: I outgrew him, that's all.
"Speak No Evil" has this exchange:
Fingers: You want to put me in a cage again?
Batman: Well, yeah.
Fingers: You're all alike—you, the doctors, Van Dyle.
Batman: Who's Van Dyle?
Fingers: You have a mother?
Fingers: I don't because of Van Dyle.
Fingers confronting Van Dyle about his mother's death, and Van Dyle's response about how But for Me, It Was Tuesday, but unusually for that trope, its not said with spite, just resignation. Van Dyle is a bit of a scumbag, but he's just a hunter, not a sociopathic supervillain. He just never thought of his prey as living beings with their own feelings.
Fingers: She was my mother!!
Van Dyle: She was just another gorilla to me...
The reveal of Payback's identity as the counselor's son who thought that getting rid of the teenager's tormentors would allow his father to spend more time with him.
In part two of "The Call" Starro who'd been portrayed since his original creation as a flat universal conqueror. In this series is simply the disgruntled victim of Superman's old foe "The Preserver". As Superman himself states, he never asked for what happened to him. He just let his resentment cloud his judgment.
The theory of Warren and Mary's divorce being caused by Warren suspecting Mary of infidelity, due to the boys' black hair and blue eyes. They are still married when Terry is about eight, implying that Warren forgave Mary for the first time, and they divorced after Matt was born. The real kicker is that Mary was never unfaithful to Warren. The boy's true parentage was due to Warren's reproductive material being overwritten with Bruce Wayne's with what he thought was a flu jab, as a secret unsanctioned government attempt to create a new Batman. So he essentially suspected Mary of having an affair with a man she'd never even met. Their marriage was essentially ruined by an outside party, yet they were still on good terms with each other in a platonic sense and treated both Terry and Matt with mutual love and respect.
Terry and Bruce's fight in the Justice League Unlimited episode "Epilogue" and especially the part where Bruce is struggling for his pills while Terry, instead of helping, just stands and watches in disgust. He tells Bruce he is insane and leaves him on the floor struggling for his meds while he is having an attack. Considering how close Terry and Bruce were on the show, seeing their relationship come to this is really hard to watch. Thankfully that scene was just a potential scenario in Terry's mind and not what actually happened. Still a horrible thing to watch.
In the same episode, we find out Ace (in a flashback) died of an aneurysm caused by years of experimentation on her. Not only that, but her last request was for Batman to stay with her until the end, since both of them had their childhood taken away.
Amanda Waller intended to create a new Batman to replace Bruce when he became too old to keep up the fight, which is how Terry was born. She also intended to have his parents killed, and hired Bruce's old fling Andrea, aka The Phantasm to do the deed, but ultimatly, she couldnt go through with it, and confronted Waller about how monstrous the whole project was and how it flew in the face of everything that Batman stood for. Waller agreed. If you know anything about Amanda Waller, it takes a LOT for her to admit being wrong about something. Not that it mattered, since Terry lost his father anyway...
Though the scene where Max officially joins Terry's team is a mix of heartwarming and funny, her genuine confusion when Terry dubs her his Alfred is a kick in the gut to anyone who loves the Batfamily's Battle Butler.
In the "10,000 Clowns" arc of the digital first comic, Bruce is trying to re-establish his relationships with Barbara, Tim and Dick. He's doing his best to develop a working relationship with Commissioner Gordon; he bribes Tim to work at Wayne-Powers by doubling his current salary and promising to put his kids through college; and the previously-mentioned appeal to get Dick just to talk to him. But Dick does not, and after Terry guilt-trips Tim into going down into the Batcave and helping him stop Joker Night, Tim is so upset by the experience that he quits the job. A year later, Terry is working with Dick instead of Bruce, and Bruce is apparently entirely alone again, with just Ace.
In Batman Beyond 2.0 Terry is (seemingly) killed by Lord Superman in the middle of telling his alternate-self to tell his version of their family he loved them and Alternate!Dick is the one ordered to make sure his corpse is strung up to send a message.
Again in Batman Beyond 2.0, it is revealed why the Bat-Family especially Bruce and Dick are not on good terms. It's revealed that Barbara was still seeing Dick and was likely having an affair with Bruce hence the picture on the Batcomputer. Later Dick is planning to propose and Barbara likely feeling guilty goes to the Batcave to tell Bruce that she is seven weeks pregnant. Bruce congratulates her and Dick, but she reveals that the unborn child is his. Some time passes and Barbara is planning to tell Dick about the love child but witnesses a mugging. She goes to help fight them off which results in her getting injured (and judging by her position on the ground she is likely having a miscarrage) at the same time Bruce tells Dick about the affair and the love child resulting in Dick giving Bruce a No Holds Barred Beat Down.
After Higgins' Batman Beyond 2.0 has jumped forward one year, the fate of new character Vigilante/ Jake Chill is left unknown... until the "Mark of the Phantasm" arc goes back one year and reveals his fate: Chill unknowingly reveals his secret to Terry, who had responded to an S.O.S. following an attack on Chill by the Phantasm. Affected by the Phantasm's fear toxin, Terry begins to beat up Chill for the murder of his father, forcing him to go into hiding. Despite Bruce's warning, Terry goes after Chill, who had been incapacitated by Ghoul's Jokerz gang. He becomes the first test subject of Ghoul's attempts at recreating the original Joker Toxin, which proves so effective it soon kills Chill after Terry appears to confront him. This new strain is so effective it can't even get cured by Terry's antidote, and Chill dies apologizing for harm he didn't intend on causing under the influence of the Toxin.
Terry forgets to turn off the recording of his time in the Justice Lords' timeline, allowing Dick to see that that timeline's version of himself had married Barbara and that they have a son together. Hurts even more when Dick and Barbara getting married almost became a possibility, if only Bruce hadn't got Barbara pregnant, which they both learned three weeks after Dick returned, when he was preparing to propose.
Dick seemingly dies stopping Rewire in the 39th issue. Fortunately, he wakes back up a few minutes later.
In a cross-media example, Superman/Batman Annual #4 is a continuation of "The Call," which has Superman dealing with everything that happened while he was under Starro's control, including Lois' death.
While it flagrantly contradictsReturn of the Joker, the ending of the Hush Beyond comic. Hush is defeated, and Bruce starts talking much more than he normally would, inviting Dick Grayson to come back to the mansion with Terry, even saying that while he knows things can't ever be the same again, maybe this is just a chance for them to speak again... only for Terry to reveal Dick had already walked away and wasn't listening.