In the episode "Indifference", Greevey and Logan confront a Child Services clerk about the case of a 6 year old victim not being followed up, despite the situation having been first reported months before the events of the episode by the child's teacher. The clerk's response is to simply pull up a listing of open cases on her terminal which runs continuously as she explains:
Clerk: This is just the city, detective. Last I heard there were over 100,000 open cases in the state of New York. We kind of have our hands full.
The entire episode "Mushrooms", in which the apartment of a normal law-abiding family is shot up with an automatic weapon because a Child Soldier was unable to read and realize he was at the wrong building. A young teenager became paralyzed from the waist down and a 11 month old baby was killed for no reason.
Any episode involving children, obviously, but one early episode, "Cradle To Grave" featured a baby freezing to death in his crib. In addition to the Never My Fault mentality being thrown around endlessly in the episode (mainly from the mother and the landlord), it's heartbreaking to see a victim that young, especially for anyone who is a parent.
Greevey's murder in "Confession". Making it even worse is it all happened in front of his wife Marie and as Logan had to listen helplessly on the phone. Then his feelings as he's speaking with Olivet at the end of the episode:
"Max's death. I accept it. But I'll never...accept it, you know what I mean?"
In the season 3 episode Mother Love, a former honor student turned crack addict has been shot dead. The trail leads first to her dealer/boyfriend, but there is no evidence to link him to it. Stone and Robinette discover that the girl had stolen from her family, including bearer bonds from her grandmother, to support her habit and suspicion falls on her father. Ultimately, they discover that it was her mother who had killed her. Performed by the incomparable Mary Alice (the Oracle in The Matrix Revolutions).
Virginia Bryant: "I looked at her, it was so hard. Those little lines of blood in her eyes, her hands full of holes. My baby... It was so pitiful. She gave me the gun. She begged me, 'Mama...put me out of my misery. Do it for me...please.' I...I gave up. I gave her what she wanted. I killed my baby."
The ending of Season 4's "Mayhem". A very socially awkward but endearing man is on trial for a string of brutal murders - he's unable to provide an alibi but both the detectives and prosecutors feel he didn't do it. Eventually, his mother reveals his alibi - he's actually gay, and was seeing his lover when the murders took place, however he didn't tell the police because he didn't want his mother to find out. However, his mother already knew, but had never told him because she didn't want to embarrass him. The obviously relieved detectives go to the prison where he's remanded to get him released - only to find out he was just killed by another prisoner.
In the Season 6 episode "Savages", we see McCoy prosecuting embezzler Paul Sandig for killing a police officer, which is a capital offense. Eventually, with his guilt beyond doubt, Sandig finally breaks down, expressing remorse and tearfully begging for his life. The guy may have been guilty of murder, but it's still pitiful to see.
"Savior" has a woman and her son brutally murdered in their sleep and the father, an unemployed alcoholic in debt, arrested for the crime. At his trial, the man broke down in tears over what happened to his family yet in spite of his anguish, still did not confess to the crime. Turns out, he didn't have to as he was innocent; it was the teenaged daughter who also was "attacked" that convinced her boyfriend to kill them to get money from her mother's expense jewelry and due to the troubled relationship between the two women.
"Jeopardy". Schiff has discovered that an old friend has become a corrupt judge when he learns that he let a guy get off on a triple murder rap once his wealthy mother offered him a large sum of money. After all the usual shenanigans that result in the bad guys being convicted and sent to prison, Jack, Claire, and Adam are in his office celebrating when Adam receives a phone call informing him that the judge has Ate His Gun.
The season 6 finale "Aftershock". Claire Kincaid getting killed in a car accident. The music that plays in the background as Briscoe gets out of the car, goes to check on Claire, and realizes that she didn't make it...
In the episode following "Aftershock", "Causa Mortis", has the case of a Happily Married schoolteacher who was abducted at gunpoint and found murdered. At the killer's trial, there was a recording of the poor woman's last moments alive as she begged the man not to kill her, telling her how much she loved her husband and showing him pictures of her children while her widower and young daughter weep openly in court. At the end of the episode, there was a moment where both Briscoe and McCoy share the feelings they have over their own mutual guilt over what happened, as well as each man wanting the other one not to have guilt:
McCoy: You know, before it happened...she wanted to quit. I talked her out of it.
Briscoe: Yeah, well...I could have kept walking past that bar.
"Double Blind" has a mentally ill college student kill a janitor. After the dust had settled in finding him and getting him to trial, it's discovered that the kid didn't kill the man because he was mentally ill but rather because he had a tumor, which a doctor who was allegedly studying his brain for research didn't care to actually do; he used the man as a means to an end to look better. By the time is was found, it had become inoperable. Had the man actually did his job, then the murder wouldn't have happened and the young man would have survived. He even confronted the doctor saying "They say I have around a year to live, maybe two if I'm lucky."
The Season 7 finale, "Terminal." Adam has been unavailable throughout much of the episode and not quite up to his usual Deadpan Snarker standard when he is around, because his wife is dying in the hospital. The final scene is him alone in the hospital room with her when she finally dies. He begins to cry.
Judith Sandler, a witness and the doer from "Survivor". Already being the daughter of Holocaust survivors and being traumatized by what her parents went through, which affected her upbringing and being afraid of the world around her, she helped to carry on the pursuit of her father's lost possessions, namely, his coin collection, which he had put in storage before he was captured years earlier. She then was more or less harassed and tricked by Ross and the detectives into searching her apartment. It's later discovered that a Swiss billionaire had already sold the father's coins and that she had killed the victim, who she thought was withholding knowledge about them, for nothing.
Lennie Briscoe in Season 8. His daughter gets arrested for drug possession and is forced to testify against her dealer, and after his acquittal she ends up murdered. He goes to the crime scene and has to be restrained from cradling her body by his partner. To see this gruff, world-weary homicide detective on the verge of sobbing just makes you ache.
Lennie: "She was my baby, Rey. What am I gonna do?"
Rey: "You're going home with me, partner."
In the Season 8 episode "Ritual", the police investigate the murder of an Egyptian man, and learn that he'd been killed after trying to arrange a clitoridectomy for his American-born niece. Not only does the poor girl have to deal with the knowledge that her dad was the murderer, but she also faces the prospect of having to live with her strict Egyptian mother, who fully intends to subject her to a clitoridectomy for the sake of family tradition. Thankfully, the DA's office intervenes, but the end result still requires her to move out of state and live with relatives that she doesn't know very well.
In the the Season 8 episode "Under the Influence", McCoy is trying a banker named Bernard Dressler for killing several people while driving drunk. McCoy is going further than usual in his pursuit of justice, trying to give Dressler the death penalty. Everyone is telling him to back off, because Jack lost his lover to a drunk driver. Then Dressler breaks down and begs for forgiveness, and Jack realizes what he's doing. A defendant in tears and Jack pausing over a sheet of paper shouldn't be that evocative...
The victims' impact statement of the slain police officer's widower in "Bad Girl":
Mr. Flynn: Dana and I wanted to have children, but we decided to wait until she was more settled in her job. I could imagine...us sitting at the table for Sunday dinner and all the little happy faces around us. I've got nothing left...I want my wife back.
"Tabula Rasa" had a father who was a Manipulative Bastard that kept his wife and two daughters under lock and key by not allowing them to make friends outside of the home or really do anything without his permission. It eventually comes to light that he abducted his children from their biological mother, who had custody, years earlier and brainwashed them against her and killed the victim by throwing her in the path of a train because she recognized him from back then. Furthermore, he admits that he never loved his second wife and only married her to give his children a mother. The real mother then is able to find them all, but due to his lies, they hate her and after he goes to prison, the younger daughter, who's still a minor, is ordered to live with her, which upsets the girl as her older sister yells at her mom, "Are you happy now, you bitch?" The episode is a true Downer Ending that gives a realistic look at what happens in tragic situations like that.
In Sideshow, Jack McCoy is questioned by someone trying to get him to reveal the name of a confidential informant, and the person questioning him tries to discredit him by bringing up both Claire's death and her relationship with Jack. Jack just stares at the man looking horrified and asks, "Have you no shame, sir?"
In the season 9 episode Refuge, Part 2, Abby breaks down in the courtroom after Carlton Radford is convicted, knowing it will help bring down the Russian mobsters who killed her friend, Toni Ricci. She later mails a copy of the verdict slip to Ricci's parents.
As Rey Curtis prepares to leave the squad to care for his dying wife, Lennie gives him a goodbye hug:
Lennie: Anything, Rey. I don't care what time it is. Just pick up the damn phone.
"Stiff", where a woman is comatose after being given spiked insulin, has the last-ditch attempt to wake her fail, the woman's daughter, who is responsible for the crime, whispers tearfully "I'm so sorry, Mom."
Denise Grobman, the victim from "DNR", who was left mortally wounded by an assassin hired by her husband, who was jealous of her burgeoning career as a judge. She is in strong denial over him trying to kill her and severely depressed over being left a paraplegic who cannot care for herself. At the trial to determine if she was competent to make a decision on her life, she suffers a breakdown on the stand:
Denise: *to McCoy, tearfully* Why do you keep on hammering and hammering?! Can't you see that everything was my fault? Walter did not do this. I've loved him for more than half of my life. When is this over? When is this over?! *turns around to face the sitting judge presiding over the case, who is also a good friend of hers* Lisa! Please, please make them stop! Just let me die.
In the Season 10 "Endurance", a mother has been put on trial for murdering her son, who suffered from severe physical and mental health problems which had obviously taken their toll on her. Upon his cross-examination, McCoy inadvertently prompts the mother to break down on the stand and admit that she had watched him have what she thought was a fatal seizure, unable to bear saving him only to force him to endure the pain and suffering he was forced to live through, and actually attempted to kill herself with her son's pills so that they would both die together before coming to her senses. The woman's tearful breakdown as she insists that she couldn't bear to see her son suffer any more is so affecting that even the hard-assed, seen-it-all-before McCoy looks shaken by it. And notably, it marks one of the few times he deliberately enables a technically guilty party to receive a lighter sentence.
"Mother's Milk" has two incompetent new parents who are raising a baby boy when he goes missing. After giving the detectives the run-around and blaming each other, the little boy is found dead. Although he was buried in a garden by the father, he wasn't technically murdered; he instead starved to death because his mother couldn't properly breastfeed him. Worse, she went to a clinic to get assistance, only for the consultant to guilt her and tell her she just wasn't trying hard enough and that using formula would be a horrible thing. There was formula in the apartment, but she didn't use it because she thought it would make her a bad mother and possibly harm her baby.
"Phobia" had a gay man brutally murdered by someone acting on behalf of his adoptive child's biological mother to take the baby back. Hearing the testimony of the man's distraught partner is hard to watch and the fact that they were devoted not just to each other, but to their son as well.
Even worse, it was revealed that the man had terminal non-hodgkin's lymphoma a year earlier that he wasn't treating, meaning that in addition to his substance abuse he likely would have died before the year was over. They killed the man for nothing.
The young man, Sammy Mireles, from "Smoke" learned that his parents sold him out to a known pedophile to pay for his younger brother's medical bills and live comfortably. The look of horror and devastation on his face when he learns the truth is unforgettable:
Mrs. Mireles: We only did this to save Davey!
Sammy: Davey! What about me?!
Mr. Mireles: Hey, you weren't the one who was going to die!
Sammy: Well, what do you call this, huh?!
In "Sheltered", it turns out that the criminal abducted his "son" a decade earlier. The man had brainwashed the kid into believing that his family was either dead or no longer loved him. When he's reunited with his mother and sister, he's downright horrified and screams at them to get away from him, not believing that they're his relatives. He spends the remainder of the episode shunning them, and even as his kidnapper is convicted and taken away, he still wants nothing to do with them. Stockholm Syndrome is real and can be incredibly hard to break.
"Identity" had an elderly man who had gunned down the greedy unemployed executive who stole his identity and entire his life savings of $400,000. How did he steal the man's money? Through an email scam he used to bilk unsuspecting people, namely the elderly, out of their money. And why did the old man have a computer in the first place, in spite of the fact he really didn't know how to use it? It was given to him by his son so he wouldn't have to deal with him or visit him, which the man brought up to him. In the end, Southerlyn felt bad for him, even believing that the son should serve some time with him.
In "Compassion", similar to "Endurance", McCoy is cross examining a pediatric oncologist who killed a man who had conned her out of money by claiming he could speak to the dead. The woman breaks down and begins babbling uncontrollably and McCoy is shocked to realize that for once, the accused wasn't presenting a bullshit defense. Years and years of watching children die despite her best efforts had taken its toll on her, and this man scamming her was the final blow.
"Married With Children" focuses on whether a woman murdered her ex-wife for denying her custody of their daughter; the victim had applied to adopt as a single mother and had sole parental rights, since the state they lived in at the time doesn't allow gay couples to adopt. On the stand, the little girl says the defendant told her the victim is just on a business trip and will be back soon - she's confident that soon, she'll have both her beloved moms back with her. The child's grandmother is in tears, and several others in the courtroom look close to it.
"License To Kill" has a young teenage boy being severely injured when he's in an SUV that's chased off the road and crashes into a restaurant. His mother breaks down when she's told that the driver, presumably her husband, was killed. The driver is not her husband, and in fact had kidnapped her son - but her hope soon turns to despair as the detectives find that her husband was one of a hunting party all murdered by the driver. Later in the episode, the boy wakes up in hospital and, after being questioned by the detectives, eagerly asks to see his dad; Green and Fontana leave his mother to explain to him. On top of everything else, the boy dies from complications of his injuries. The vigilante who ran the car off the road gets away scot-free, since the media hailed him as a hero and the jury is firmly on his side.
The secondary victim in "The Family Hour" comes from a very screwed up past. She was habitually abused by her father, a powerful politician, and her socialite stepmother, she then abused her younger half-brother, she develops a drinking problem by the time she's 11 due to her father pimping her out to his friends, she ends up marrying an abusive man herself, she ends up killing the stepmother and ends up being brutally murdered by her father.
Season 20's "Dignity" has a woman explain to the jury of how her terminal child was born and eventually died in her arms. The jury, Connie, and an officer are seen wiping away tears.
Season 20's "Fed" has Anita attending the funeral of Rey's wife who wanted to be buried in New York. It's already sad but gets worse when they talk about their last conversations with Briscoe before his death.