Nathaniel Sr's death, which kickstarts the whole series. Later on, Ruth breaks down while throwing dirt into the open grave.
There's also David breaking his composure immediately after the funeral as he rebukes Nate for attempting to assert an influence over the family after living independently for so long.
David: Just do me a favor, okay? You got out... stay out.
Claire's breakdown in Nate's arms after Gabe blows her off.
The episode where David takes upon his shoulders the responsibility of organising the funeral of a gay bashing victim. SOB.
Gabe discovering his brother accidentally killed himself with a gun. Without us actually seeing anything, he stares into the room in utter horror, only able to say "Fuck!" over and over.
Nate telling David of his arteriovenous malformation, a potentially fatal brain condition. David's the first person he tells, which is a marked contrast to how cold they were in the first season.
Much, much later that season, Nate tells Ruth that he's seriously ill on the week of his surgery. She expresses her frustrations that he didn't tell her earlier because: "There just so many months I could have loved you better."
Also in the second season is the episode "The Invisible Woman", about a woman who had virtually no people in her life. Ruth gathering her family so that Emily Previn has a service might count as heartwarming, but when she breaks down at the end of the episode in front of her children's photos after realizing she's not so different from Emily, it's downright heartwrenching.
Bernard's death and the silent reaction of the Chenowiths.
The moment when Arthur's recording a voice message for his now grown-up cousins he used to babysit and he suggests that they get an e-mail so that they could actually keep in touch. Is it meant that they don't reply him? Poor lonely guy.
When Nate buries Lisa. Alone. In the middle of nowhere.
Sara revealing to Ruth that her free, bohemian lifestyle was never truly her own choice after all: She lost the love of her life in her twenties, turned out to be infertile and all the parties and happenings she's throwing for her artist friends are mostly an attempt to make up for her own lack of talent.
Nearly the entirety of All Alone the tenth episode of the final season, the episode after Nate dies:
Ruth and David preparing Nate's corpse, and their subsequent fight.
Maya asks Brenda at least twice 'Where's my daddy?' in such a sad and innocent little voice. As if that wasn't sad enough, Brenda decides not to sugar-coat it like her mother suggests and says flat-out 'Daddy's dead. He's not coming back'.
Nate's funeral on its own is a massive tearjerker. David gets a panic attack and is unable to finish his eulogy, and, later on, can't leave the car for Nate's burial
Ruth refuses to let Nate's burial go on without David and patiently waits with him until he's composed enough. Also doubles as heartwarming.
The burial itself. The Fishers and the other close guests shovel dirt into the grave and barely keep their composure.
When Brenda hands Maya over to Ruth and tells her she'll be happier with her.
Brenda coming home from Nate's burial to what she thinks is an empty house, but to her surprise, Billy's waiting there for her. She just crumples into sobs after holding back for most of the episode.
The last episode is full of tearjerking moments: everyone toasting for Nate and especially Maya toasting for her Daddy, Brenda and Ruth's conversation on the stairs, and the very beginning, which isn't a death, unlike in all the previous episodes, but a birth.
The final montage. Six Feet Under ends with Claire driving off to New York to start a new life. As she drives, she imagines how everyone's lives might turn out... and, since this is Six Feet Under, it ends with the deaths of everyone in the main cast. Set to "Breathe Me" by Sia.