This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Star Trek: Voyager
What Harry and the aliens of the week were put through in "The Thaw" is a cross between this Fridge Horror and Nightmare Fuel. Let's put this into perspective: the aliens were the innocent victims of a natural disaster. The simulation that was supposed to take care of their subconscious minds accidentally created an entity from their fears, "the Clown". Then the Clown went about happily torturing them for nineteen years. Then, despite the Voyager crews best efforts (mainly the Doctors) only two of them survive and escape.
The Doc probably has it pretty bad in this, despite his abilities in the simulation he's still ultimately unable to save one of the very people his seeming invulnerability was meant to be used to protect.
Chakotay cradling the dead Janeway's body in "Coda", even if it turns out to be a hallucination. The anguished cry he lets out is absolutely heartbreaking.
The frozen bridge in "Timeless".
More than that, future Harry's breakdown over not being able to get Voyager home...and then his jubilation when he manages to save them at the last moment.
Fridge Tearjerker: Even though it's not shown, one of the frozen bodies on Voyager is little Naomi.
Tuvok mourning Suder at the end of "Basics, Part II".
Suder in general. A stone-cold serial killer, he recovers. He realizes what he's done and how terrible it is and how terrible a person it has made him. Yet circumstances force him to take on that role again. In the end, his death in the process was a mercy.
Tuvix, trying to rally some support among the bridge crew. He's about to be executed, and he's literally committed no crime.
The whole ending sequence of that episode, where Janeway has to un-merge Tuvix back into Tuvok and Neelix, is one of the most harrowing (and controversial) moments in the entire franchise. Janeway's face afterward makes it even worse.
Regardless of where you fall on the ending of "Tuvix," the scene where Kes goes to Janeway after he's asked her to interfere on his behalf is heartbreaking.
Kes: Captain, Tuvix has asked me to speak to you on his behalf. But I can't.
Janeway: He shouldn't have put you in the middle of this.
Kes: But I am in the middle. I have been since the moment of the accident. I don't know how to say goodbye to Neelix and Tuvok. I know this sounds horrible, and I feel so guilty for saying it, and Tuvix doesn't deserve to die, but I want Neelix back. (breaks down crying as Janeway hugs her)
"Threshold" may be one of the worst episodes of any Trek series, but still gives us a marvelously acted moment by Robert Picardo as the Doctor starts to put his hand of Kes' shoulder after Tom's death, then backs off.
The whole death scene is incredibly moving between all three of them, Tom, the Doctor, and Kes. For a couple of minutes, you forget you're watching "Threshold" and focus on the fact that Tom is dying and they can't save him.
One of the assimilated personalities that Seven channels in "Infinite Regress" is an older woman who was going to meet her son, a Starfleet lieutenant, at Wolf 359 when the Borg attacked. Unaware of the nine years since then, or that she was herself taken by the Borg, she begs Janeway to help her find him and tell him that his mother is all right.
It's Fridge Tearjerking, but there's also the personality of the girl who's about Naomi's (physical) age - we see Seven acting like a kid, smiling and just looking for fun. The stark contrast to standard Seven, combined with the knowledge that she never got to be like this before in her life...
Tuvok saying goodbye to Janeway in "Year of Hell, Part II".
Basically all of Year of Hell. The once proud and beautiful USS Voyager battered again and again until it is little more than a barely functional hulk while the crew took heavy casualties is hard to watch. thank god for the Reset Button.
The death of the Alpha Hirogen Karr near the end of "The Killing Game" two-parter, he did do terrible. But his acts of cruelty were out of the simple desire to save lives by preventing the Hirogen from dispersing themselves to far across the galaxy. Even Janeway herself admits his intentions are in everyone's best interests when he admits this. She also appears genuinely saddened when he dies.
An amnesiac B'Elanna beginning to remember her old life and wondering if the similarly-amnesiac Tom will ever love her again in "Workforce".
Seven: You must comply! ... please ... you are hurting me. One: You will adapt.
At the beginning of the episode, Seven is looking in a mirror and practicing smiling. After One dies, she looks in the mirror again and just stares.
Seven trying to come to grips with glimpsing her holy grail in "The Omega Directive".
Seven: For 3.2 seconds...I saw perfection. When Omega stabilized, I felt a curious sensation. As I was watching it, it seemed to be watching me. The Borg have assimilated many species, with mythologies to explain such moments of clarity. I've always dismissed them as trivial. Perhaps I was wrong.
The Doctor's breakdown when learning what really happened during "Latent Image", and his attempts to deal with it in the end, with the crew keeping a round the clock vigil to ensure that he avoids another system crash.
It goes deeper than that. At first Janeway coldly claims that the Doctors memory was altered because she and the crew saw him as nothing more than a malfunctioning piece of technology. But it's far too easy to hear the blatant lie in her voice. Just watching her, B'Elanna, Tom, and Harry's behavior throughout the episode and you can see that they didn't erase his memories because they were inconvenient. They did it because they care about him and they didn't wont to see their friend suffering.
One thing the episode doesn't focus on much is Harry's thoughts on the situation. No doubt he feels (though totally unjustified) responsible for the Doctors mental breakdown and suffering.
The ending of "Unforgetable", only Chakotay's writing everything down on paper manages to prevent a complete Downer Ending.
The episode, "Mortal Coil" counts as this for poor Neelix. After dying (and staying dead for 18 hours), he's revived and brought back to life. Sounds like a reason to celebrate, right? Wrong. Neelix believed that after death, his spirit would journey to a place called the great forest, reunite with his dead loved ones, and journey together to the afterlife. What did he experience? Nothing. The rest of the episode follows him as he tries to make sense of what happened, and realizing that his life-long beliefs about the afterlife may have been a lie. Even worse is when he tries a vision quest, and encounters his long dead sister, who says the afterlife is a lie, and mocks him for believing in it. As one of the series writers put it, "What would be worse than having your own dead grandmother come back and say, "You know, there is no God. This is all a figment of your imagination, you're going to die, and there's nothing after. You disappear, and that's that. See ya!" Poor Neelix...
Made worse by the fact that this episode aired on December 17th, 1997. Two years later, however, we got a good TearJerker episode based on a similar subject, only B'Elanna is on the receiving end, where she goes to Klingon Hell to successfully rescue her mother.
Even worse? This was written because Brian Fuller, the show's lead creator/writer, was having a Creator Breakdown. He realized that he was gay which went against his very conservative Catholic upbringing. Just about everything Neelix went through in that episode was what Brian Fuller went through.
That poor old crazy codger in "Resistance" who thinks Janeway is his daughter. The fascistic Mokra have so thoroughly destroyed him that there's hardly a scrap of a man left.
The Doctor or rather a backup copy of him recovered 700 years in the future gets one in "Living Witness". Not only does he struggle to cope with the fact that the Voyager crew are long dead by this point, but also the realization that his very rediscovery is bringing centuries-old tensions on the alien world he's on to their breaking point. He eventually becomes so distressed that he practically begs to be deactivated. Fortunately though, it gets resolved.
The end of the episode "Hunters", when the signal from Starfleet destabilizes and the relay network Voyager had used to contact the Alpha Quadrant goes offline. For the first time in three years, the crew had contact with home, and they were getting letters from their friends and family—given some of the letters' contents, a heartbreakingly mixed blessing. (Dear Kathryn, I held out hope longer than anyone and then I moved on and married someone else.) And all too soon it's snatched away. Tom and B'Elanna's reactions are especially TearJerker-y, with B'Elanna finding out that all her Maquis friends are dead or imprisoned and Tom dreading hearing from his admiral father only to never get a chance to read his letter.
In the episode "Real Life," when the Doctor's fictional daughter Belle is fatally injured in a sports accident. At first he ends the program at her deathbed, unable to stand it. Tom convinces him to go back and see it through, reminding him that real families don't have that choice. The Doctor and his family—at that point, reprogrammed to be more difficult—gather at Belle's bed, and the Doctor has to tell his daughter that she's going to die. It ends on the Doctor and his family pulled together in grief after Belle passes on.
In "The Raven," Seven remembering her last moments before she was assimilated.
"And then the men came. Papa tried to fight them, but they were too strong. I tried to hide. Maybe they wouldn't find me because I was little... but they did. And then Papa said we were going to crash and the big man picked me up. And then suddenly, we weren't on the ship anymore; we were somewhere else. And then I became Borg."
In "Extreme Risk", Torres dealing with depression and her utter inability to feel anything, so she starts hurting herself. Her utter apathy and numbness while Neelix tries to make her happy by giving her banana pancakes shows how far she's fallen.
In "Dark Frontier," the crew is planning a risky raid on a Borg sphere and Janeway asks Seven to go over the Hansens' log entries from the Raven. Seven isn't eager to study the belongings of people she considered "misguided," but it's Neelix of all people that makes her reconsider.
"A faded holo-image. That's all I've got left of my family. A picture of my sister. (holds his chest) Except, of course, what I keep in here. What I wouldn't give for a treasure trove like this."
Of course, then Seven starts reading the logs and finds that her parents weren't just unlucky, but that they took many unnecessary risks in studying the Borg.
"My parents underestimated the Collective. They were destroyed. Because of their arrogance, I was raised by Borg."
Seven tells the Borg Queen You Killed My Father. In reply nearest drone steps forward. It's Seven's father.
In "One Small Step"
"The Yankees...In six games."
Commander John Kelley's log entries in general. He died alone in a subspace anomaly God knows how many light years away from any other human, but he didn't see it at a failure, instead gathering as much information on it as possible in the hopes that one day, humanity would find him.
"Someone To Watch Over Me"
The Doctor falls for Seven of Nine, but in the end Cannot Spit It Out. The writers didn't want to develop the Doc-7 ship, and ended the series with the unconvincing Last Minute Hookup between Seven and Chakotay.
In "The Gift", Kes' powers surge so suddenly and violently that she has to leave the ship or she'll tear it to pieces in her ascension to energy being. Tuvok tries to ground her with a mindmeld, but it doesn't work, and he and Janeway have to rush her to a shuttle. The only goodbye they can manage is Janeway radioing the bridge and informing them that Kes has to leave, with only a brief shot of their stunned faces. Afterwards, Tuvok dresses in his ceremonial robes and lights his meditation candle in the window as a tribute to her, looking out into space.
"Lineage," pretty much as a whole once it starts digging in. First of all, it's got flashbacks to a camping trip with her father, overhearing him complaining about living with two Klingon women, later revealing that he left B'Elanna and her mother about two weeks later. These flashbacks are also filled with young B'Elanna feeling isolated and alone among her human cousins because of her Klingon heritage. Meanwhile, in the present, B'Elanna learns that she's pregnant. Because of the dominance of Klingon genetics, her daughter is going to have the distinctive cranial ridges. B'Elanna goes to extreme lengths, including reprogramming the Doctor, to do genetic modifications that will remove them, make her look human. When Tom confronts her, she breaks down in Sickbay, because of her fears that because she was part-Klingon, that was what drove her father away, and she doesn't want to drive Tom away. Then Tom assures her that he isn't going anywhere and wouldn't be against more children.
Zimmerman's tale of the EMH Mark 1 in "Life Line". He had a vision of holographic doctors saving lives, and he created a program that, without question, is a fantastic doctor. But because he based it on himself, people complained about the bedside manners and the entire series was reassigned to menial labor. So now there's hundreds of holograms with his face doing demeaning work, all because one flaw outweighed all the benefits. Thankfully, the Doctor is still out there doing what he was meant to, which is some consolation.
It's hard to not get a little teary eyed in "Future's End, Part II" when the Doctor is given his mobile emitter and steps outside for the first time in his existence. He stands in the middle of downtown LA and just looks around, amazed by all the things he's experiencing.
Despite his Scrappy status for most people, Neelix's back story, revealed in 'Jetrel,' is heartbreaking. Talax was at war with the Haakonians, and he was a draft dodger, refusing to join up. While he was there, the Haakonians unleashed the Metreon Cascade on the moon of Rinax, wiping out the entire population, Neelix's family included.
Tom Paris being being demoted to ensign and spending a month of solitary confinement in the brig in 'Thirty Days'. He deserved the punishment because he did disobey orders but for the person who was such a life of the party 'people' person this was a very low point for the character.
"Endgame (Part 1)", Admiral Janeway visits a degeneratively-ill Tuvok, fighting back tears that she'll change the past to change this present outcome, and thus, never see him again.