The German and English versions of "The Dark I Know Well".
Martha and Ilse clinging to each other in every version, and the various ways the song has been staged since then (including one in Vienna where Ilse helps Martha symbolically stab a pillowand it bleeds.
Martha and Ilse's actresses frequently get contacted from fans who suffered abuse, and too many people seem thankful that it captures helpless/embittered rage instead of sadness or fear. The actresses always nearly spit the lines that quote their abuser, especially "child, you're a beauty."
In the original play:
The Masked Man last words to the protagonists, "To you [Melchior] the doubt about everything, to you [Moritz's ghost] the certainty about nothing."
Although Moritz already brought his eternal inevitability, Melchior gives Moritz some meaning in Moritz's life after all. Melchior tells him "no matter if my personality was to change a hundred times, you will probably be [my closest friend]" Melchior walks off with the Stranger leaving Moritz behind. Moritz is saddened to rest in eternal rot but realizes that he can rest, straighten his grave with dignity, and sleep with a smile on his face.
The reprise of "The Word of Your Body". While the two boys are kissing each other is incredibly sweet considering all the dreary stuff going on at the same time, all of the chorus standing around them singing "You're gonna be wounded" gives the dark implication that their lives are not going to be easy in the future.
Hammered in by Andy Mientus' Hanschen, who looked back smugly at Ernst's voice as he leaves with the deaf boy, in a "ha ha I've got him now and there's not a thing you can do about it," manner. Given exactly what he was masturbating to in My Junk...
"Left Behind." The most poignant, heart wrenching Grief Song ever.
Herr Stiefel breaking down and sobbing at Moritz' grave after Melchior touches him. Especially when you consider how stoic and cold he has been for the whole play.
"You watch me, just watch me. I'm calling... one day all will know."
In the original play Melchior's giving Moritz's ghost a farewell (after the ghost deviously tried to drive Melchior to suicide) and telling his friend something among the lines of "if my personality was to change a hundred times, you might be my closest friend". The Masked Man last lines "To you [Moritz] the soothing consciousness that you have nothing, to you [Melchior] the enervating doubts about everything." Although Moritz is upset that he will continue to rot in his grave, he realizes he can smile in dignity as he lays down to eternal rest. This can also be partially listened to in the 2001 Workshop.
The painful conversation between Wendla and her mother about her "little girl dress". "But Wendla, you are already — in bloom." (And in the Workshop Cast, when Frau Bergmann finds out about the pregnancy. Her mother screaming at her and Wendla just completely uncomprehending, crying and saying that she didn't understand what happened or why she was bleeding afterward.
The reveal of Wendla's pregnancy is tragic in any production, particularly when she realizes (after having to ask her mother to confirm it) that her sexual encounter with Melchior was what caused it. That is the saddest part simply because you realize that unlike some of the other characters, she had no way of changing her fate - not only was she not in control of her relationship with Melchior, she was never even informed of the dangers and then shamelessly blamed for the result despite the fact that she begged her mother at the beginning to tell her about sexuality.
At Moritz's funeral when each are taking their turns to put flower on the open casket. Everyone reacts the same, except Ilse. It usually depends on the actress, but she seems to be the only one to cry.
In some productions, Martha not only cries, but kisses the flower before dropping it in the grave. Given the fact that it is established that she had a crush on Moritz, this adds a whole new tear jerker to an already very sad scene.
Frau Gabor's letter to Moritz, in productions where she's portrayed as writing it in good faith — it doesn't do much to help him, and it's clunky, but it's clear she really does love him and she's trying with the only tools she has (reassuring him that even famous businessmen and scholars did poorly in school, that it's not the end of the world, that he doesn't have to run away or do anything rash or hurt himself)to keep this boy safe. It's still not enough, but she never had the tools to do the job in the first place. Likewise, the scene where Melchior's parents have to decide what to do with him after the news comes out of what happened to Wendla — whatever may have happened in any given performance of the show, they think their beloved son, who they have striven to raise liberally and as a free thinker, is a hooligan and a rapist. Their decision to send him to a reformatory really is rooted in a genuine desire to help him, they just don't have the tools to do that either. All the Adults Are Useless content in the plotline is frustrating and annoying to many fans, but the moments where it shines through as more than just "adults suck!" are hard. None of the parents, even the ones who try to do a good job, have any more idea what they're doing than the kids; were they ever shown any better?
On a totally different end of the parent scale — Moritz's father's response to him getting kicked out of school, especially in the workshop cast. Imagine how scared squirrelly, dreamy Moritz must have been of such a stern man. Then, his father not only yells at him and makes perfectly clear his anger and disapproval, he hits him. Several times.
During one production, in the song "Those You've Known," Melchior was center stage with the knife he'd jacked from the reformatory and on the platform behind him had Moritz and Wendla standing and singing to him. Ilse sat between them. A couple of times Melchior would hold the knife against his throat and Ilse, who just lost Moritz, would stand up and move to stop him.
The way Melchior broke down and screamed "No!" repeatedly at Wendla's grave.
The reformatory boys (in the Spanish-language production) holding Melchior down to take Wendla's letter from him look an awful lot like they were going for a gang rape. Frau Gabor's line about "degenerates" and "genuine criminals" doesn't help matters, either.