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Tear Jerker: Justified
"Reckoning" gets two to more or less bookend the episode:
The beginning of, when Raylan walks into the house where Aunt Helen's body lay, and
Towards the end, with Raylan about to execute Dickie, explaining exactly what his Aunt Helen meant to him, and because of everything he remembered she did for her, finds himself unable to kill him.
During "Brother's Keeper," Loretta insisting to Raylan that she has a father around to scare off unwanted suitors left this troper a little teary - seeing as Raylan and the audience already know that he's not.
Raylan talking Loretta out of shooting Mags in revenge for killing her father by telling her how much it will change her in the season two finale, and in particular:
Raylan: Ask yourself what your daddy would want you to do.
Loretta: (starting to cry) I want him to be here to tell me.
Mags Bennet may be a wicked, wicked woman, but the look on her face when Raylan tells her she can't see Loretta is heartbreaking
As is the scene where she commits suicide, partially because she seems to be intentionally mirroring her actions from the scene in the first episode of the second season where she poisoned Loretta's father, arguably the most villainous thing she did all season
Winona in "When the Guns Come Out" giving Raylan the shaft again, this time probably for real. It's especially painful because Raylan seriously began to think about retirement for her and it turned out she was lying through her teeth about being okay with his job. It was going on for weeks. Art, Tim and Rachel knew. Raylan didn't.
Ella May, visibly traumatized after Trixie's death in "When the Guns Come Out," and after Krystal's death in "Loose Ends." Delroy's indirect role in the women's deaths, combined with his callousness to Ella May's suffering, made it even more heartbreaking.
Watching Mrs. Dodd after she finds out that her son Tanner is dead.
In "Guy Walks Into a Bar," listening to Quarles tell Donovan about the sexual abuse he endured as a child. Subverted when we later see Donovan bound in Quarles' bathroom.
That truly awful moment in the season 3 finale when Quarles tricks the boys' mother into getting out of the van and makes them drive off without her. The heartbreaking moment is seeing her run after the van in vain, tripping and falling, crying for her sons.
To that end, Raylan's tranquil fury at the death of a fellow cop, especially after he finds out Arlo shot him, possibly because he thought the cop in the hat was Raylan. His face as the episode closes says it all.
Raylan telling Hunter that Arlo reconciled with him and told him he loved him on his deathbed. Hunter knows it's a lie and Raylan is hardly making any effort to conceal that fact.
Boyd, after Ava is arrested breaking into the beautiful suburban house he and Ava were going to buy, just to look out at the backyard from the porch.
In "Over the Mountain", when Raylan takes Kendal into protective custody. Daryl and Danny are horrified, then angry that Raylan wants to take their little brother away. Kendal reluctantly leaves with Raylan to save his brothers, who were about to enter a deadly fight with Raylan to protect the boy.
The death of Hot-Rod Dunham, of all people, who dies while his Friendly Enemy, Alex Miller, looks on sadly.
Say what you will about Danny Crowe, but the scene where he brings a wreath and flowers to his dead dog's grave, and tells Raylan about how he saved said dog from a puppy mill is pretty sad.
Seeing Wendy in "The Toll". She's heavily beaten up, her hair is even messier and after Kendal takes the fall for Daryl, she is practically catatonic and sobbing in a pathetic way.
YMMV even more than usual, but Daryl's rant to Wendy in "Restitution" where he criticizes her poor parenting skills and lack of involvement with the family, calling her out on the fact that she's the one who handed Kendal over to Daryl, knowing full well what her brother was like. It's a stark look at family dysfunction, and when Wendy demands to know why Daryl thought she wouldn't understand, his agonized response says it all: "You don't want to know, Wendy. You don't ever want to know."
The same episode has Jimmy's death and Boyd's reaction to it.