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Tear Jerker: BlazBlue
Ragna's flashback in the beginning of his Calamity Trigger story mode. Dear God, no wonder Ragna is the way he is.
In one path in Rachel's story, where she realizes it's too late for the world to be saved and she'll be forced to keep reliving the events until Ragna succeeds, she begs Ragna not to give up or accept his fate. She then she travels back in time, lamenting on the fact that she can only continue observing.
Lambda-11 is just one big Tear Jerker from start to finish. You will probably never find such a depressing character in a game.
Her Story Mode starts during the events of the Calamity Trigger prologue, from Lambda's point of view, with the varied tests being run on her. She is clearly in pain from the testing, and is screaming in her mind, but she is unable to do anything to stop the procedures. Going through her recovery by Tager from the Ikaruga ruin, to the eventual wipe of her memories and original personality by Kokonoe, and it becomes readily apparent how much of a Woobie she is; just about every waking hour she had was ruled by pain and helplessness, and she was trapped in that until she functionally died in Kokonoe's lab. All the while, she's crying and begging for help.
Hell, even her gag reel's a Tear Jerker, or extremely dark humour. Don't tell me you didn't shed a tear (or laugh, or both) when Kokenoe accidentally threw away the rare, puppy-like insect she'd adopted and erased her memory of the diversion that caused her to encounter it. The worst part is that if Kokenoe knew about it, she may well have started treating Lambda more like she treats Tager (i.e. more like a subordinate she cares about than an Empty Shell).
Also on the subject of Lambda, we have Relius' opening fight in Darkness Visible - Relius vs Lambda... at the... Heritage Museum... The prelude to the fight involves Relius coming upon Tager and Makoto during their meeting, and Kokonoe sends Lambda as interference while the aforementioned bail. The outcome is bad enough - Lambda loses, gets apprehended, and everything goes to hell - but the circumstances make it worse. While Relius had some interest in Tager and his artificial Armagus, the intel Makoto was carrying couldn't be ignored, either, and Kokonoe had to choose whether to sacrifice either of them or Lambda, with no fourth "safe" option. Having to give up Lambda in exchange for those two was one of the toughest choices Kokonoe had to make in her life, and like That Which Is Inherited it's going to weigh upon her for the rest of it. And since she may have inherited some of Jubei's longevity, unless she makes a Heroic Sacrifice of some sort (fat chance), death is going to take its sweet time in finding her.
Lambda-11's eventual Heroic Sacrifice during Continuum Shift's Final True Ending, where she gets between Hazama and Ragna just as Hazama is about to finish him off. With her dying breath, Lambda gives him her Idea Engine, allowing Ragna to overcome the restrictions Hazama is placing on his Azure and ultimately save the day. Lambda-11 so far is the only playable character to be Killed Off for Real.
Litchi and Tsubaki both performing a Face-Heel Turn at the end of Continuum Shift. And um, why is it Tear Jerker? First, considering that before signing her Face-Heel Turn, Litchi has been thinking of her happy times with Tao and Bang, you know she clearly dislikes turning her back on them AND hates Hazama, but not only Arakune's situation, but her degrading condition basically forced her into it. As many would say, if you put yourself in Litchi's shoes, you know it's a sad and heavy decision, even for her... not a happy choice based on selfish obsession. As of Tsubaki, first she just realized that her superior Hazama was utter evil bastard, just for her blindness to kick in, and then when she tried to find consolation with Jin during her encounter in his story, Jin wasn't even giving the answer, which culminated with Phantom possessing her and finalizing her turn.
To compound the matters for Litchi, she has actually asked Kokonoe for help, but Kokonoe just flat out refused, too busy of thinking to kill Terumi by her own hands. When you squint it, it just looks like a Distressed Damsel (she mentally is, needing help to cure her corruption and dependance over Arakune) who is refused of the only help she knows and the only path for her is to act on herself with the remaining option to stay alive. No matter what you say, if you're a Distressed Damsel and when you ask for help, the response you got was "Go away, I'm busy.", it is a pretty depressing thought. Making matters worse for her, when she tried to justify her distress and desperation to Rachel, Rachel's response was pretty much not helping and calling her stupid for accepting NOL/Terumi's offer. Damn it, somebody please give Boobie Lady a hug for a change, rather than calling her selfish, obsessed and stupid.
Arakune's bad ending in Continuum Shift's story mode. He finally remembers Litchi and realizes that his subconscious memory of her has been one of the few things keeping him from truly losing it (well, more so anyway). He then cures her of the erosion that would've turned into something like himself (if it didn't kill her) and erases her memory of him so she can move on with her life. Just goes to show that there's still something of a heart in that blobby mass, which MAY count as a Crowning Moment of Heartwarming... until it is realized that considering Litchi's other bad end... it turns out because Litchi will degenerate into a mess at best and is incurable, not even by Kokonoe.... which means... Arakune just committed a Senseless Sacrifice due to him not knowing the true nature of the Boundary corruption fully. Way to poison the heartwarming, Arcsys - you'd have to be a total jackass to think succumbing to an Alzheimer's facsimile is preferable to risking a thick, but still cleanable, stain upon your morality!
Oh God, Hakumen running into Tsubaki, the story "Old Man's Tale." The stone-hearted warrior lightens for the first time. The first moment of heart-cracking comes when he asks to see Tsubaki's face, which is covered by a hood and a mask. After she reveals it, Hakumen touches her face like a lover. This is the man who claims to be the reaper of the sins of this world. He speaks from experience, trying to warn Tsubaki against the use of the Izayoi. Hakumen then tells a beautiful story about how he fell in love with an old childhood friend, how he left her side, and how she followed him only to die at his side. She changed his life so much, that he named a technique of his combat style for her. That woman was an alternate Tsubaki, and Hakumen hasn't seen her in nearly a century. Watch it and cry.
And if that doesn't get you crying, the Drama CD's reveal that Jin was basically forced to watch Tsubaki die and it was at the hands of Nu-13's LegacyEdge, who was in a rampage of unjustified jealousy thinking Ragna was "cheating" on her with Tsubaki. Depicted here◊ for your viewing displeasure.
Hakumen actually wills himself into this timeline and runs into Hazama and Relius, eventually picking a fight with them. Shortly in, Hazama is screaming for Relius to help as Hakumen beats his ass, and when Relius eventually sends Ignis in, Hakumen rocks her as well. All is good until he is eventually dragged back into the Boundary, leaving the two villains to clean up and be on their way. Losing Tsubaki once was bad enough, but being cheated of the opportunity to save her like that, knowing she is going to die and he can do naught about it? Geez, it sucks to be Hakumen.
Makoto's bad ending. Trying to locate Jin when he goes missing, Makoto loses her way and runs headlong into Relius. The two fight, and things don't go well for Makoto, with Relius instructing Ignis to pin Makoto down, leaving her at his mercy. Relius begins reaching into her mind and torturing her by forcing her to relive all her worst moments, like the racist abuse she suffered at the military academy, all while Makoto is screaming and desperately pleading for mercy. Injured, paralysed and humiliated, she can do nothing to stop Relius from mockingly laughing as he begins to rebuild her soul and turn her into a weapon like Ignis and Nirvana.
Even worse, there is a section of the ending where the character portraits disappear, and all we can hear is Makoto's sobbing and pleading, with Relius describing in detail what he's doing to her. This whole thing amplifies the effect that there is something horrible happening offscreen.
Ragna's bad ending in Continuum Shift. He finally loses control over the Azure Grimoire, transforming him into a new Black Beast. Apparently unaware of what's going on and drifting in a half-conscious state, Ragna kills Jin and goes on a world-destroying rampage before being stopped by Noel and Hakumen. Waking up paralysed and on the verge of death, he can only look up and ask Rachel to stop crying as she gives him a tearful goodbye. Ragna dies alone and in agony, blissfully unaware to the extent of his failure.
Tsubaki's bad ending in Continuum Shift, in which she begs Noel for forgiveness for her secret jealousy, all the while going blind due to using too much of the Izayoi's power, eventually passing away in Noel's arms.
Not to mention the ending to the Wheel of Fortune drama CD, which ends almost the same way. Except Hazama turns up, laughs at Tsubaki for dying, and then kicks her dead body afterwards.
And yes, there's also a Tear Jerker when you play Arcade mode. Play as Mu-12, get beaten by Makoto and you'll get a win quote involving Makoto sobbing and desperately trying to get Noel (not Mu) to wake up, even promising to let her play with her tail as much as she wants. Oh, and getting up means you get Mu to beat the crap out of Makoto and possibly kill her. Drat.
All of Carl's bad endings Nirvana, who is actually his sister Ada, gets ripped apart in both. In CT's Carl Bad ending, Litchi doesn't show up (Because Tao never beat Carl, and he never showed up in Litchi's clinic.) So Ada protects him from Nu's attacks. In CS, Hazama brutally rips her apart, while Carl cries, and begs him to stop.
Litchi's Arcade run and eventually in Chronophantasma. On top of being beaten by Rachel, she was brutally told by Rachel the consequence of insisting on saving Arakune and joining NOL: Kokonoe considered her crossing her Moral Event Horizon and declared her an enemy that she can kill, and her acts fighting Bang enabled Relius to snatch his Rettenjou and quicken the Day of Destruction, since it is capable of creating an anti-Seithr nuke, and it's mostly Litchi's fault for being insistent. Even if Rachel had a point, it's still too much for poor Litchi, learning that she hurts more than she helps, she was played for chumps by evil, she ruined her bonds with her other friends that cared for her (especially Kokonoe)... and the scene ends with Litchi on all four, genuinely crying out of remorse. It's times like this you may be tempted to give Boobie Lady a hug... her allegiance be damned.
The climax of the Chronophantasma story, it's hard to watch Bang Shishigami breaking down witnessing that Litchi has remorsefully sided with Relius to create a world where Lotte Carmine lives, meaning that every of his fantasies of her being a perfect Purity Sue was shattered, hard, and he couldn't even lift his finger to defend from Litchi's attack. Then it was also compounded with Carl, his 'Apprentice #2', also threw his lot to Relius just for the cure of Ada. And not just from Bang, you'll also feel sorry for both Litchi and Carl having to beat up Bang despite apologizing as they already considered him a great friend, but they have been too invested to their goal which had to lie in Relius' palms of all things that they can't stop. Though Bang managed to persevere, succeed his mission and later both Litchi and Carl could reverse their misfortune of being manipulated by Relius, it's pretty sad that their friendship could never be the same again... And to compound this on Bang? His 'Apprentice #3', Platinum, died against Terumi outside his sight, meaning that there's only Tao remaining that he knew as his Apprentice...
The resolution as well. Ragna has finally destroyed Gigant: Takemikazuchi and even saved Nu-13 from its core! Well... cue the cruelest Yank the Dog's Chain to commence: Nu rises back and backstabs him and the Imperator uses a trigger word that turns Ragna into a beastly abomination nearly similar to his CS Bad End form, and all he could do is to urge Jin, Noel and Celica to run off as he eventually went complete berserk, and attacks Jin and Noel who stayed to stave him. All that's known was that Jin was heavily wounded to the point of bedridden and Noel was thankfully just lightly wounded. But Ragna's gone, now a mindless beast and probably a core of the Imperator's Takemikazuchi Embryo and will have to be put down for good by the next game... our hero, ladies and gentlemen. Damn it, Ragna...!
To twist the knife even further: This is after Ragna vowed not to use the Azure Grimoire's power as much and become a protector as Celica suggested. So for him to not only succumb to his fate against his will, and hurt people, just makes it sting further.