Both Alex and Kara are obviously still not over the respective end of their relationships, and Barry and Iris's jolly marriage isn't helping things.
Felicity (unintentionally, in an emotional outburst) loudly turning down Oliver's marriage proposal, causing a very unpleasant moment for both of them.
Prometheus-X is Earth-X's Tommy Merlyn. Oliver's face tells us all the emotions he's going through at this moment. And then, at the end of their confrontation, Tommy kills himself. Oliver essentially had to watch his best friend die in front of him again.
Oliver-X is obviously distressed when finds out Prometheus-X is dead. Just goes to show that, even in a universe where they are terrible people, the brotherhood between Oliver Queen and Tommy Merlyn is strong.
After learning that the Earth-X Reverse Flash is actually Earth-1 Eobard Thawne, Barry and Iris wonder if they will ever truly be rid of the man.
Earth-X Felicity is a prisoner of a concentration camp, complete with a star on her uniform as a "Jewess."
The entire scene of the heroes about to be executed by Earth-X Quentin (before Earth-X Snart saves them). You can see the desperation, the sheer horror in their faces and the inconceivability that this could really be their end.
The death of Martin Stein and everything surrounding it, which is a tearjerker both In-Universe and out.
First, there's Jax. Jax is adamant about not giving Stein the serum that will sever the link between the two of them, which would allow Jax to live while killing Stein. Jax is completely willing to die along with Stein, but the professor won't let that happen. He points out that Jax has his whole life ahead of him, and that no one lives forever. Jax very reluctantly gives Stein the serum, and once he drinks it, he tells Jax that he hopes his life is as joyous and full of love as his was. And then he takes his last breath, and Jax just breaks down completely.
After the cut to black, we return to see Sara walk into the room and she stops in shock. She is able to hold her composure, but it's very clear that she's greatly saddened. Jax leaves, and Sara just stares at Stein's body for a few moments before kissing her dead teammate on the forehead.
After that, we cut to Barry and Iris, with Iris shaking her head in silence and Barry figuring out the news by himself. The two walk up to each other and embrace, grieving the loss of Stein without saying a word. We then see Caitlin and Cisco, with the former wrapping his arm around the latter, and the two just stand there, also silently grieving. It had been a while since any of them had any significant interactions with Stein, but he was still their friend nonetheless.
We then see Ray, Vixen, Zari, and Steel. Ray is holding up a black-and-white picture of him and Stein in Old West outfits, and it's very clear that he's holding back tears as Vixen places her hand on his shoulder. While Ray is the most distraught (understandably so, since he had spent the most time with Stein), the other three are visibly upset at Stein's death as well.
Finally, we see Jax knocking on the door of the Steins' house. Clarissa answers, and she's initially delighted to see Jax. But a distraught Jax can only apologize, and once it dawns upon Clarissa, she breaks down crying in Jax's arms. Lily walks up to the two, and once she figures out her father is dead, she also breaks down into Jax's arms, and all three of them kneel onto the ground, crying over the loss of their family member.
After the forces of Earth-X are defeated, with Overgirl and Dark Archer dying while Thawne promptly leaves, a funeral for Stein is held, with the Legends and Team Flash in attendance. Jax says some words before telling Clarissa and Lily that he's so sorry for all of this, and Clarissa tells him that he was family, too. Even Mick sniffles, which he tells Citizen Cold is allergies. Clarissa shovels some dirt onto Stein's coffin, muttering a final farewell. Then Sara does so, thanking him for believing in her. Caitlin does so while saying to "tell Ronnie I miss him", and then Barry does so while thanking Stein for opening the portal from Earth-X to Earth-1 and allowing him to return to Iris.