* From "Aliens in a Spaceship" [[spoiler: Bones and Hodgins have been burried alive by the Gravedigger and convinced they are going to die despite their PlotArmour]]
--> '''Hodgins''': ''[[ItHasBeenAnHonor It's been an honour]].''
** Lots of Hodgins in this episode. Other notable moments include:
*** His admission to Angela at then end that he's too scared to sleep anymore.
*** His admission to Bones before she operates him.
--> '''Hodgins''': I'm crazy about Angela. Over the moon, stupid in love with her.
** Also, when they realize that [[spoiler:one of the twin brothers had killed himself in hopes of giving the other brother enough air to survive.]]
*** Zack's inability to understand ''why he should tell the twins' father'' made it 50 times worse. The concept is heartbreaking for everyone -- but for many real-life twins, it's downright TERRIFYING.
* Booth's [[spoiler: anguished declaration of love]] to Bones in "The Parts in the Sum of the Whole". And her heartbreaking reply.
--> '''Booth''': ''Hear me out. Alright? You know when you talk to older couples who have been in love for thirty or forty or fifty years, it's always the guy who says I knew. I knew. Right from the beginning. I'm that guy, Bones. I'm that guy. I know.''
* Pretty much the entire last portion of the Season 3 finale.
** Zack's tear-filled confession of the crimes and revealing the location of Gormogan..
** Brennan going through the logical process that led Zack to do what he did... [[spoiler: and then pointing out that he risked everything so that he wouldn't hurt Hodgins.]]
** The gang looking in on Zack through the hospital window.
** The fact that all of Zack's favorite things were items giving to him by his friends, including Brennan's acceptance letter for Zack's internship.
* Bones' breakdown in "The Doctor in the Photo".
--> '''Bones:''' "I missed my chance."
* "The Hole In the Heart": [[spoiler: The death of Vincent Nigel-Murray]] and the team's reaction to it, including Bones' [[NotSoStoic breakdown]].
** "[[spoiler: I don't wanna go. I love it here.... Please don't make me leave....]]"
*** What makes that dialogue even sadder? [[spoiler: Bones thought he was talking to ''her''.]]
* The entirety of "The Ghost in the Machine". It's told from the point of view from the victim - A fourteen-year-old boy. Just his age itself is sad, but when you hear what everyone has to say to him (Or his skull, rather) and realize that he hears it too... Hell, Brennan even cries for him. And she '''never''' cries over victims.
* [[spoiler: Cam talking to Sweets about Michelle in "The Babe In The Bar". She asks him why she should be going to him for advice about her adopted daughter when he doesn't even take care of a pet. Come "Mayhem on a Cross", we find out that he was adopted by a loving couple when he was a child, and that he knows better than anyone why she should listen to him.]]
** In a sad but also heartwarming way, the fact that he tells her she's doing great. Coming from [[spoiler:Sweets]] who knows what it's like to be adopted, that's probably the highest praise he could give her, and she doesn't even know or understand.
* So many in "The Man in the Fallout Shelter":
** The team's brief visits with their families, separated by a glass wall, while they're quarantined in the Jeffersonian during Christmas, set to "Have Yourself A Merry Little Christmas" sung by Music/ToriAmos.
*** Dr. Goodman seeing his two young daughters. It's one particularly sweet because you mainly see Goodman as the administrator and occasional DeadpanSnarker who has to corral the team as best he can.
*** Hodgins seeing his main squeeze, who leaves lipstick marks all over the glass while he smiles.
*** Angela with the gentleman we later learn is her father.
*** Booth seeing Parker.
*** Bones standing off to the side, alone, in stark and painful contrast to Zack's large, loving family come to visit him.
** The end, where Bones is able to tell the fiancée of a man murdered in 1959 what really happened to him, and that he'd never abandoned her. And that he inadvertently left her a legacy
** The final scene with Bones and the present... [[spoiler: which her parents had left for her when they had disappeared around Christmas. She was so angry with them for abandoning her that she never opened it... but she still kept it. The look on her face when she opens it is almost painful to see.]]
** "Don't you wish someone had told ''you'' that your parents were dead -- just so you can finally stop wondering?" -- "Yes."
* Cam [[TheDeadHaveNames reading out the names of the slaves who died in the sinking of the Amalia Rose]] as their portraits light up one by one behind her is incredibly moving, especially when she chokes up on reaching the one with her great-grandmother's name.
* In the season seven finale, Brennan [[spoiler:takes Christine and goes on the run after being framed for a murder]]. Booth manages to just catch the car driving off and says in the most heartbreaking little voice [[spoiler:"That's my family..."]]
* Cam breaking down in tears while telling Hodgins that the hair recovered from [[spoiler:Dr. Brennan's]] trunk matches the victim's.
* Booth's eulogy for a homeless veteran [[spoiler:who died rescuing three people from the Pentagon on 9/11]].
** That entire episode. That entire fucking episode.
* Finn, Colin, Fisher, Arastoo & Wendell telling each other their memories of the day, and when they first learnt of the 9/11 attacks.
* "The Finger in the Nest," in which Brennan decides to adopt Ripley, the fighting dog at the center of the case. However, since the dog has killed a person, the judge in the case orders it put down - which she doesn't find out until after she's already purchased toys, bedding and a personalized collar tag. Brennan's expression at the news, and then her halting attempt to say something over Ripley's grave, is heart-wrenching.
* The comparing scars scene in "Mayhem on a Cross" where Bones reveals that her foster parents locked her in a car for two days
* "The Pain in the Heart". Everything involving [[spoiler:Zack]].
* "The Goop on the Girl". The scene near the end where the radio broadcaster [[spoiler: gives his final show about how it's really his fault that the man died, because of all the hate he's spreading]]. His words were so touching, you'd have to be inhuman to not tear up at that.
--> [[spoiler: "These will be the final words I broadcast. And I hope they're the words you remember the best. Peace on Earth."]]
* Bones says she finds the idea of a woman burying her son "heart breaking". Booth tells her “You are the one who always says that the heart can’t break because it’s a muscle. It has to be crushed,” she replies “Well, isn’t it heart crushing?”
* "The Boy in the Shroud". The entire episode, but especially the end when 'Bring on the Wonder' plays.
* "The Superhero in the Alley". The ending, when Angela completes the final page of the murder victim's semi-autobiographical comic book? Yeah.
* "The Graft in the Girl". Amy, the teen daughter of Booth's boss, has cancer, which it turns out was caused by a bone graft from a bone with cancer. After further investigation it turns out there are more people with cancer from the same donor (whose bones were illegally harvested). In the end the murder is solved and, but Amy is still going to die.
* In "The Foot in the Foreclosure" Booth's grandfather, [[BadassGrandpa Hank]], is introduced. He's a constant source of snarky remarks and awesomeness. Also, he [[spoiler: accidentally burns down Booth's kitchen while making dinner]]. His speech to Booth after [[spoiler: the firefighters leave]] is really emotional. You can hear in his voice that he ''knows'' that now the roles have switched and his ''grandson'' will have to take care of ''him''. This hits a little too close to home for those who have seen their grandparents needing help to do previously mundane things.
* Their goodbye in the final episode of season 5 caused some tearing up as well, for sure.
* "The Singing in the Silence" - a deaf mute runaway girl is found covered in blood. It turns out [[spoiler: she had to kill a man who tried to kidnap her and take her back to her violently abusive parents, who it turns out in fact kidnapped her from her real parents when she was a toddler. It is an incredible AdultFear episode for any parent, to imagine their defenceless three-year-old being taken and used so horrifically that she's unable to trust anyone, and her only happy memory is of a stuffed rabbit...]]
* When Arastoo is infected with a deadly disease and the only one who can help is the murderer, seeing the normally stoic Cam just utterly break down begging him to help is utterly heartwrenching.
* From the season 8 finale, "The Secret in the Siege". [[spoiler:Booth, who originally accepted Bones' marriage proposal, had to call it off due to Pelant threatening to kill innocent people if he didn't (or if he told Bones about it). Bones' reaction (once she gets out of Booth's view) is ''heartbreaking''.]]
* The part in "The Archeologist in the Cocoon" where the team demonstrates the fate of the Neanderthal/Homo sapien remains from 25,000 years ago: [[spoiler:It was a family murder scene - a homo sapien mother, a neanderthal father, and a hybrid daughter were killed by a homo sapien interloper. The mother and father both died killing the interloper, while the 3 year old daughter was left to starve to death because neither species would adopt her. Their only comfort was that the father crawled to and cradled the mother while he bled to death and she suffocated, and the daughter curled up with them at the end, so that they could all be together. Booth outright calls it [[HumansAreBastards The World's First Hate Crime]].]]
* Season 9's episode "The Spark in the Park". The victim's father is the physics-professor version of Dr. Brennan, extremely intelligent but with few apparent social graces. At the end, Brennan comes back to check on him, and he is writing vector calculus equations. Bones realizes and the professor explains that each one represents a different phase of his daughter's life, starting with "At rest in her crib", going through crawling, walking, somersaults, ice skating, her gymnastics career... and finally again, at rest. Bones tearfully remarks that this is "the most beautiful thing I've ever seen...more beautiful than a speech, more beautiful than a photograph"...
* Season 9 episode "Big in the Phillipines," where we find out that [[spoiler:Wendell has Ewing's sarcoma, a rare bone cancer]]. Brennan's reaction and struggle to tell Wendell is also more of a Tear Jerker when you think about what happened to Zack and Vincent, two other interns Brennan valued the most. Another Tear Jerker (which triples up as it is both a Moment of Awesome and a Moment of Heartwarming) is when Wendell says he [[spoiler: doesn't think he wants to seek treatment]] until Booth tells him that he still has a life ahead of him with a wife and kids.
* In 9x15, "The Heiress in the Hil", Hodgins learns about [[spoiler:his estranged brother, hidden away in a full-time psychiatric care facility by his parents before he was born.]] He goes to visit him and they're having a nice conversation, when Jeffrey has a psychotic break and starts ranting about his delusions. The look on Hodgins's face is ...
* And let's not forget to mention when [[spoiler:Cam adopts Michelle]] that one moment when she [[spoiler:goes up to her room to get the salt shaker]].
* Booth and Brennan sharing "scars" from their childhoods as a way to comfort Sweets after discovering [[spoiler:whip scars on his back]].
* [[spoiler:Bones tearfully telling Booth that she can't let go of her relationship doubts despite how she feels about him.]]
* The sixth season premiere, "The Mastadon in the Room", in a good way when Hodgins and Angela are talking about [[spoiler:their baby]].
* As a man who has been on the tail end of [[spoiler:a rejected marriage proposal]] what happens to Booth at the end of "The Daredevil in the Mold" is particularly jarring.
* "The Shallow in the Deep", when Angela [[spoiler:gives faces to all of the slave ship victims.]]
* "The Blackout in the Blizzard". TJ Thyne can make the chemical composition of coins bring tears to your eyes.
-->'''Hodgins:''' You hear that something has a one in a thousand chance or one in 10,000. ''*sobs*'' But I guess it's like the lottery, right? Someone always wins, you know?
-->'''Angela:''' That sounds like good news.
** Then he just can't even speak and just looks at her, tears streaming down his face, and Wendell quietly leaves the room.
* [[spoiler:Sweets being brutally killed]] in the last minutes of the season 10 premiere.
** The following episode takes it UpToEleven. Note that prior to the last between-seasons TimeSkip, Christine still wasn't speaking yet (a season 9 episode's B-plot actually had Bones worried about how long it was taking for her to start speaking), so these are the first complete sentences the viewers get to hear her speak.
-->'''Christine:''' I'm ready!\\
'''Bones:''' Ready for what?\\
'''Christine:''' [[spoiler:Uncle Sweets and Daisy]] said they'd take me to the park today.\\
* cue Bones and Booth looking uncomfortably at each other, trying to figure out how to explain that [[spoiler:Sweets is dead]]*
* In "The Bones On The Blue Line", Sweets is sitting next to a guy who just a text saying he's now cancer free. He then proceeds to tell Sweets how he's going to travel the world and sleep with exotic women, things he'd been putting off because of his cancer. He got thrown into a handpole on the subway, killing him.
* Seeing Booth relapse on his gambling addiction is heartbreaking for anyone who has had loved ones go through similar relapses.
* The sick and exhausted mother from “Stargazer in the Puddle”. She had a daughter who sadly suffered from a condition that left her in a myriad of health issues: unable to hit puberty while simultaneously rapidly ages the body, while leaving the affected person with the mentality of a six-year-old child. The mother was under heavy medications, and one of those drugs was experimental. It left her feeling worse than before and her own mental health began to deteriorate. She knew no foster home would take her. She ends up killing her own daughter with an overdose on her old medication and alleges to have drowned her daughter and it was ultimately done out of mercy and love. In a stroke of cruel irony, her medication belatedly began to work right after her daughter’s death. The scene between Brennan and the distraught mother was so heartbreaking, the way the mother looked at the rock her daughter had written on and broke down crying: “I love you”.
* Learning that Clark's girlfriend of eight years broke up with him in 'The Ghost in the Killer,' leading him to be crashing at the Jeffersonian. Seeing the normally straight-laced and confident squintern hitting his lowest point and this lost is hard to see.
* The pain in Brennan's voice when Booth tells her to take Christine and go to Max's, because the operatives behind the conspiracy are coming after them.
--> '''Booth:''' I love you.
--> '''Brennan:''' Don't you die.
* Hodgins [[spoiler: getting stuck in a wheelchair]] is bad enough on its own but seeing him taking out his anger at this turn of events on the team to the point of verbal abuse, culminating with him telling Angela that she should leave if she can't take it, is heart-wrenching.
* In "The Movie in the Making", the tribute scenes to Zack, Vincent and Sweets will definitely tug at your heartstrings.
** Additionally, the devastation of the victim's estranged father is [[TearJerker tear jerking]].
* The Reveal that the Puppet Master is [[spoiler: Zack Addy. Adorable Zach is now a serial killer, who wants to kill his pseudo-family that was his Jeffersonian colleagues. The fact that official interviews hint that there's a chance that Zach is only crazy, not a serial killer isn't enough to remove the heartbreak at the moment.]]