Quinn and Gideon's death. She's just so shaken and manic and terrified.
Fitz getting shot. The whole episode.
When Huck gives a passionate speech to his fellow spies to get them not to kill another spy and they do anyway.
Mellie's intense, sincere apology to Olivia after she catches Fitz basically drunkeningly feeling her up in an elevator. There's no plea to keep quiet or accusations of seduction—Mellie seems to really, truly feel bad for Olivia. Doubles as unintentional guilt slinging.
Several of the scenes involving Abby and/or David in Nobody Likes Babies, but the one where David charges in and accuses Abby of stealing an important piece of his evidence, his voice cracking as he says he trusted her because she said she loved him takes the cake. Especially when she insists she does, and he refuses to let her touch him.
Fitz: Did I do this to you? Or have you always been like this? Because if it was me, I'm sorry. I'm sorry.
The woman Olivia tries to help in 3.03. Her son was shot by the FBI under suspicion of being a terrorist, and the investigation concluded that he was one. She was so desperate to find out what happened that she takes people hostage with a bomb strapped around her chest, as she refuses to believe her son was guilty and she wants to know what actually happened. She was right the entire time. Her son was in deep cover infiltrating Al-Queda, and due to inter-departmental screwup the FBI didn't know that and killed him during a raid. Her son was actually a hero. But she can never know that, because there are other assets there too who would be killed if word got out. Olivia is informed of this by the president, and she has to lie to the poor mother and tell her that her son was guilty of terrorism, in order to protect the other assets who had infiltrated Al-Queda with him. Her son was a hero, and nobody - not even his mother - would ever know he wasn't guilty. This breaks his mother. The result? The woman allows her hostages to leave, before slamming the door shut behind them and detonating the suicide vest.
In 3.03, when Olivia learns Huck is still trapped by his training, she comes home and goes off on Ballard, trying to find out why he's there. Her father and the president ring, but she throws both phones to the ground. The whole episode seemed designed to break her, and it works.
"Big Jerry," Fitz's dad, rapes Mellie. There's nothing to really add to that.
Jake's monologue at the beginning and the end of "No Sun on the Horizon." He had a very unhappy childhood, has no family now, and being part of B6-13 might be slowly breaking him. His lack of family also explains why both Fitz and Olivia are so important to him.
Seeing Cyrus break down sobbing at the press conference announcing the capture of his husband's killer, or at least the person he thinks is his killer, to the point where he has to be hugged and escorted off by the president is heart-wrenching. Even if he is severely morally ambiguous, we see through the episode he really did love James and is completely lost now.
All of Fitz and Mellie's scenes in "Randy, Red, Superfreak and Julia." Mellie actually lies down at the grave of her son. We also find out Fitz attempted suicide at some point. The details are vague for now.