Murdering her sensei, one of two people at the Facility who showed her any love and kindness, while under the effects of the trigger scent.
And all of this being done to a child. Even worse, Zander Rice is doing all of this not because the project requires it, but as Revenge by Proxy on Wolverine for killing his father while escaping from Alkali Lake. Laura's only crime is being created using Logan's genetic material. The pain and suffering she endured at the Facility is utterly heartbreaking.
While not as graphic, the flashback scenes in her debut episode count. Nothing like watching a little girl cry as she's being mercilessly trained into a killing machine.
The climax of X23: Innocence Lost. "You are not a weapon. You are a child. You are my child..." *sniff* The repetition of the same words in the sequel, X-23: Target X, has a similar effect, especially when you realize that Laura never got to read the letter the first time around...
The second flashback in Target X almost trumps the letter itself. There is something inherently heartbreaking about a thirteen year old girl weeping in the snow besides her mother's body, it is magnified by the realization that said girl killed her in a chemically induced Unstoppable Rage (and knows it), but what manages to combine the sadness of the moment with the horror that was her life to that point is what she whimpers to Dr. Kenney's cooling corpse:
Even worse is what she says during this scene in Innocence Lost as for a moment, Laura stops being a weapon and is just a little girl again in need of her mother:
"Please don't leave me."
The Killing Dream: Laura's encounter with her inner self during her Battle in the Center of the Mind while trying to prove to the demon tempting her that she does have a soul. Not only are we revisited with the horrible things done to her by the Facility, we learn that despite all of this, Laura was never fully broken. One small act of mercy, sparing Martin Sutter's ( actually Zander Rice's) son when Rice sent her to murder the whole family, allows her to defeat the demon and escape his influence.
Doubling as a Crowning Moment of Heartwarming, Laura's goodbye to Megan in Target X. Just before they depart, Megan gives her a locket containing pictures of herself and her slain mother.
Laura's confrontation with Logan at the end of Target X. She has been so beaten down and broken by everything she has been put through that she's decided the only way out is that she and Logan both must die. And as she explains why, Logan just resigns himself to death for his complicity in the Weapon X program, but pleads with her not to throw her own life away because her lack of choice makes her innocent.
Her dismissal from X-Force at the end of Second Coming. First, her immediate thought is that Wolverine is punishing her. Second, Laura's entire life up to that point had been defined by having someone to issue her orders — to the point that Wolverine notes early in the series that he suspects Laura was incapable of recognizing Cyclops's invitation as a choice and not a command. She is completely and utterly lost at the thought of having to find her own way, to the point that she is pleading and begging Logan to give her an order to follow. It's utterly heartbreaking to see her facade of strength crack and break down, and is a painful reminder just how truly damaged she is.
Laura's frustrated breakdown in All-New X-Men #35. She tries so hard to find something to believe and hope in, something better than the terrible things she's seen, done and had done to her. And then she gets dumped into the Crapsack World that is Ultimate Marvel, reinforcing to her that it never gets any better. The fact this is set before Wolverine's death but was released after, with the reader knowing that she's soon going to lose one of her central points of guidance and direction doesn't help. However perhaps the worst part of the scene is no matter how much he wants to do something, all Warren can do is stand back and let her vent her rage and heartbreak and not be able do a thing to help her because she still struggles with letting people in.