Shaak Ti's death. After losing her duel with Starkiller, she tries to convince him that he could beso much more. When Starkiller stubbornly insists on his loyalty to Vader, she sadly remarks that he will eventually find out the harsh reality of the Sith before falling backwards to her demise.
Shaak Ti: You are Vader's slave, but your power is wasted with him. You could be so much more... Starkiller: You will never convince me to betray my master! Shaak Ti: Poor boy. The Sith always betray one another. But you'll find out soon enough...
This exchange between Starkiller and PROXY shows that, even in the eyes of his apprentice (who knows nothing about Vader's backstory), Vader's existence is an agony.
PROXY: I hate being him. Starkiller: I think he does, too.
Vader's first betrayal of Starkiller.
Starkiller has successfully defeated a Jedi Master, and expects that he will finally be able to do what he's spent his life preparing for: helping his master destroy the Emperor. Instead, Starkiller gets painfully stabbed in the back. His expression of agony, horror, and betrayal is heartbreaking, especially when you remember that Vader is the closest thing to a father that Starkiller knows. In the novel, he's in full-on denial until the Emperor orders Vader to kill him, and Starkiller is completely helpless to stop Vader from following through.
When the Emperor commands Vader to kill his apprentice, Starkiller desperately appeals to his master, insisting that they can defeat Palpatine together. Vader looks from his master to his student, just like he willwhen he finally chooses to redeem himself. Here, however, he savagely beats the helpless Starkiller while Palpatine laughs sadistically and cheers him on, ultimately throwing him out into space to (apparently) die.
In the novel, Palpatine is only present through PROXY, and when the Emperor cuts the transmission, the droid looks stunned and shaken.
Also in the novelisation, Juno is helplessly watching all of this through a hacked video feed. She's left horrified by Vader's cruelty, and is subsequently arrested as an accomplice to Starkiller's "treason".
Meeting Kento's Force Ghost. Especially sad in the novel, where it's made clear that before this meeting, Starkiller had all but forgotten his biological parents. The novel, this comes at the end of a horrifying sequence where Starkiller sees himself as a cyborg monstrosity fighting and brutally killing Kento. The novel also changes Kento's line, having him use Galen's name (the first time that Starkiller can remember ever hearing his real name).
Kento: I never wanted this for you. I never wanted any of this for you. I'm sorry, son.
Juno discovering that Starkiller is gathering Rebels under Vader's orders. She looks and sounds so betrayed.
Vader's second betrayal of Starkiller is arguably even crueller than the first:
Everything seems great. The Rebel Alliance is officially formed, with Starkiller as it's leader. Even Kota seems to have found a new life. Then Vader arrives and calls Starkiller "his apprentice", ruining the trust he'd built up in his new allies, before violently attacking him.
Vader's total lack of remorse when he tells Starkiller that he never planned to betray the Emperor, and that he basically sees Starkiller as completely expendable, is a major gut punch, demonstrating that Vader has fallen so far that Starkiller's Undying Loyalty means virtually nothing to him, and he's perfectly willing to kill his apprentice, whom he raised from childhood. This man used to bea hero.
The last thing Starkiller has to say? "Without me, you'll never be free."
In the novelisation, the first thing the battered and barely conscious Starkiller says to Juno is to tell her his true name, which he's only recently discovered and embraced as his new identity. She breaks down crying after hearing this, devastated by the death of PROXY, Vader's treachery, and the apparent end of the Rebel Alliance.
Starkiller: Juno. My name... My name is Galen.
PROXY making a Heroic Sacrifice to save Starkiller from Vader. He had been repaired by the second game, but that doesn't make his selflessness in the first any less heartbreaking.
Starkiller's death at the end of the first game.
Juno's POV in the novel demonstrates that she's had a very hard life, growing up with a harsh and unloving father (with whom she was so miserable that she joined the Imperial Academy at 14) and being manipulated by Vader into causing a massive ecological disaster. She's dealing with these issues throughout the book, and just when it looks like she and Starkiller are forming a real romantic bond, he dies.
In The Ultimate Sith Edition, finding PROXY's broken remains on Tatooine. Also, the death of Obi Wan Kenobi and Luke Skywalker's fall to the Dark Side.
What makes it even sadder and one of said Starkiller's worst Moral Event Horizons is that he simply casually tosses him aside to join the junk afterwards.
Starkiller actually sounds hesitant in speaking with Proxy, especially when asking for his help. When Proxy helps him leave the room, the man that used to be Galen Marek softly tells him, "thank you" before he leaves.
The Force Unleashed II
Starkiller's POV in the novel has him constantly reminding himself, whenever he has memories of his past or something that happened in the first book/game, that he isn't the original Starkiller. Whether he is or not, it's clear that being told he was a clone has left some real scars on his sense of self-worth.
Behind-the-scenes notes give the fate of one of the failed Starkiller clones:
Lead Cloning Technician: Curious. One of the more stable test subjects began weapons training today. A training droid shorted out and wouldn't project the training program. He was having no problem cutting down all the other droids, who appeared to be living human beings, but he refused to attack the damaged droid. Flat out refused. Instead he smiled at the droid, and then started mumbling over and over: "proxy, proxy, proxy".
From Bad to Worse: That droid proceeded to brutally beat the clone, who couldn't bring himself to fight back against the machine that resembled Starkiller's oldest friend.
In the novel, when Kota tries to call him by his real name (Galen Marek), Starkiller cuts him off, insisting that he's just a clone, a "bad copy" of the original Starkiller.
Vader's callous abuse of the various clones of Starkiller is yet another harsh reminder that the good man who was Anakin Skywalker is, at this point, completely gone. He even tries his best to convince Starkiller that his love for Juno is an unacceptable weakness, implying that he's either abandoned the love his former self had for Padmé, or that this belief is driven by the painful memories of losing her and what he became in trying to prevent her death.
The scene where Starkiller enters the Dark Side Cave and sees a vision of Juno. He tries to embrace her, but she dissolves into smoke. He clutches his chest, his heart breaking.
Juno's whole plotline in the novel is quite sad, as she is still coping with losing Starkiller and finds herself totally unable to move on. A friend she made as a Rebel tries to ask her out at one point, but she can't bring herself to say yes, feeling that he deserves someone better and that she'll never fully get over Starkiller.
While making his way through the cloning facility in the second game, Starkiller starts hearing Juno and Kota's voices tormenting him. By the time he manages to shake off the hallucinations, Starkiller's on the verge of a breakdown.
"Juno": Who are you?
Starkiller: Juno, it's me!
"Juno": You're a monster, a thing.
Starkilller: [on the verge of tears] Juno, please!
"Kota": You're Vader's puppet. Just a body filled with the memories of a dead man.
A scene in the novelization, where an unconscious Starkiller remembers his mother's Heroic Sacrifice to save her family and as many Wookiees as possible from Trandoshan slavers.
In the sequel's Dark Side Ending, the last thing Starkiller sees before he dies is Juno's dead body.