From "Aliens in a Spaceship" is when they realize that one of the twin brothers had killed himself in hopes of giving the other brother enough air to survive.
"Aliens in a Spaceship": 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 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... 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".
"The Hole In the Heart": The death of Vincent Nigel-Murray and the team's reaction to it, including Bones' breakdown.
" I love it here.... Please don't make me leave...." This troper is usually quite stone-faced, but she chokes up even thinking about that scene.
That is the only episode this troper has ever seen (it was for work) and she was getting misty as well. Geez.
The episode The Plain in the Prodigy made this troper cry so hard it has never been rewatched since it's initial viewing and it still makes me choke up just thinking about it.
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.
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 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.
"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 Tori Amos.
The end of "The Man in the Fallout Shelter", 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.
"The Man in the Fallout Shelter": Towards the end, with Bones and the present.
"The Man in the Fallout Shelter": "Don't you wish someone had told you that your parents were dead — just so you can finally stop wondering?" —- "Yes."
Cam 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 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 "That's my family..."
Cam breaking down in tears while telling Hodgins that the hair recovered from Dr. Brennan's trunk matches the victim's.
Booth's eulogy for a homeless veteran who died rescuing three people from the Pentagon on 9/11.
Finn, Colin, Fisher, Arastoo & Wendell telling each other their memories of the day, and when they first learnt of the 9/11 attacks.
The episode where the spirit of the dead 14 year old boy who just wanted to impress his crush is very Tear Jerky to anyone. The spiritual element, the "kid" element, the future he could have had, everything. It's written to make you cry.
"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 Zack.
The Christmas episode of 2009. The scene near the end where the radio broadcaster 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.
"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.
The 100th episode. The Parts in the Sum of the Whole. That final scene when they were SO CLOSE to getting together but Bones couldn't do it and she pushed him away.....
Their goodbye in the final episode of season 5 caused some tearing up as well, for sure.
"The Doctor in the Photo" in season six. The car scene when Brennan tells Booth about the epiphany she's had (that she "doesn't want to die with regrets" and "made a mistake" in rejecting him), and then breaks down and SOBS at his response. Their subsequent conversation and watching her slowly pull herself back together just made it worse.
"The Singing in the Silence" - a deaf mute runaway girl is found covered in blood. It turns out 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 Adult Fear 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... sniff...
Vincent's death. "Please don't make me leave, I love being here..."
From the season 8 finale, "The Secret in the Siege". 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: 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.
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 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 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 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 ...