Animorphs/Tear Jerker

Given the incredibly dark nature of the series, was there ever any doubt that there would be tear jerkers?

Unmarked spoilers ahead.

Applegate's letter in respond to criticism of the series finale. (Spoilers abound) It makes you feel bad for feeling bad- that is to say, for not liking the end. Because what she says is true, people die in war, people break up in war, people change with war.

Alright, let's get this out of the way:
== The end - Rachel, Jake, Tobias and Tom. ==

For the whole of the series, it was Jake's intention to free his brother from enslavement from the Yeerk in his head, instead of killing what was an incredibly dangerous enemy as well as his brother. In Rachel's final battle, Tom's final words - "JAKE, STOP HER!" - drive home the tragedy of the situation. Even Tom didn't think Jake would go so far as to have his own brother killed. Jake's later narration doesn't help:

Jake: Tom was dead.
And I wondered how I was going to explain it. I had ordered my cousin to take out my brother. How was I going to explain that?
Silly to think of that then. Silly and stupid.
All those years, I had fought to keep us safe, always with the desperate hope that I would save my brother, that he'd come back, that he'd be Tom again. That was why I'd enlisted in this war to begin with. I was going to save Tom.
Tom was dead. The Yeerk in his head was dead.

Rachel's final moments also aren't pretty. Knowing she's about to die, she demorphs so that she can smile at her love interest, Tobias, who morphs human so that he can cry for her (hawks don't cry). Her last words are to him: "I love you." A polar bear then unceremoniously grunts, <You fight well, human,> and then kills her with a single blow.
And then take it ten minutes further, when we get back in Jake's head and find out that his first thought after seeing Rachel die was, "I wish that Tobias had just come after me right then. I wouldn't have stopped him. I would have welcomed it."
The descriptions by Marco of what the aftermath of the war did to Jake were depressing.

The problem was, he didn't want anything. Except for Tobias to come back. For Rachel and Tom to be alive. For the chance to unlive one fateful moment when he gave the order that doomed seventeen thousand defenseless Yeerks.

- Later, Marco also says this to Cassie after she asks about how Jake's doing:

"He doesn't put flowers on [Rachel's] memorial or whatever, there's always lots of those. He goes when no one's around, late, after hours. The guys at the gate let him in. He parks and just kind of sits there like he's hanging out with her. I don't think he talks to her. Sad as it is to say, I wish he did. Talking to a dead person is better than not talking at all. He sits there for an hour, sometimes two, stares out at the ocean. Watches the sun go down. Then he leaves. Sometimes I think he's waiting there hoping Tobias will show up."

Tobias' appearance at Rachel's funeral is easily one of the biggest tear jerkers in the entire series. His wordless insistence that he be the one to see to his love's last resting place is heartbreaking.

You know this page should be renamed K.A. Applegate Mind Rapes= Tobias.

I read a spoiler about Rachel's death, so I braced myself and didn't cry at the scene. I was being tough the whole book, but when they named the ship after her, it was impossible to resist the tears anymore.
Rachel's realization that, due to the fact she allows the others to maintain their self-image as good guys by doing their dirty work, she is only a good guy by association and isn't much better than the Yeerks she's fighting.
- The Ellimist conversing with Rachel, in another dimension and book, during her last instants of life. One last reassurance to someone resigned to be a dark Designated Hero:

Did it matter? In the end. My life and my - my death - did it change anything? Did I matter?
Yes. You were brave. You were strong. You were good. You mattered.
Yeah. Okay, then. Okay, then...

- All of the Auxiliary Animorphs dying. They were so happy to have been given a second chance, even if it meant fighting the Yeerks, and they just wanted to live, but Jake told them to fight. For this troper, this was Jake's crossing the Moral Event Horizon, even if it did help them win the war.

Everything else

After a particularly gruesome battle, the kids find a human-Controller that Jake mangled during the fighting. Dying slowly and unable to escape the host body due to injuries, the Yeerk pleads the kids to help him, but they leave instead, fearful that more reinforcements will arrive. As they go, the Controller says, "I'm dying. I'm scared... Does that make you happy, Andalite?" After a pause, Jake replies hoarsely, <No. No... It doesn't make me happy.>
#23, The Pretender. Tobias finds out through an elaborate scheme of Visser Three that Elfangor was his father. The entire scene where the will is read out loud is very tough, but throughout the whole thing, Tobias maintains a completely straight face. It's therefore an even bigger sucker punch when Tobias says the only reason for that was that he forgot how to use facial expressions, as a hawk.
- Then his finding a private back alley so he can morph human and cry.
The last sentence of #38, The Arrival.

"Cassie held my hand, and in the darkness, where no one could see me, I cried."

Pretty much everything about Marco and Eva.
It starts early. In the very second book in the series, Rachel acquire the morph of a friend's pet cat to infiltrate their house because she suspects that Melissa is a controller. She's wrong. It's her parents. As Controllers, they don't have any feelings of warmth or love for their daughter. This troper broke down as Melissa confided to Cat!Rachel "why don't they love me anymore?"
- It Got Worse. When her father (under control of his Yeerk) realizes that Rachel isn't a normal cat, thinking her to be an Andalite, he captures her and starts to take her away. Melissa freaks out, running across the yard and screaming, tearfully asking what her dad's going to do with her beloved kitty. He ignores her until she's right in front of him, and...

Melissa: "You didn't hear me? But Daddy, I was crying.
Controller: I uh...didn't notice you.
Melissa looked like she'd been slapped.

- And all this just makes a scene later in the book, when it's revealed Chapman and his wife became Controllers with the caveat that the Yeerks would not do the same to Melissa, all the more gutwrenching. Even the suggestion that the Yeerks might renege on the deal is enough to make both parents wrest control of their bodies back and start screaming in rage - even though they've been prisoners so long their free will itself has begun to entropy.
A certain passage from "The Andalite Chronicles" becomes even more heartwrenching with the help of Murray Gold. (starts at 0:58)
I found #19 - The Departure to be pretty much one big tear jerker.
In The Capture, Jake gets infested by Tom's former Yeerk and he has to be isolated for 3 days to strave the Yeerk to death. During that time, the Yeerk torutures Jake mentally, but the worst moment is when the Yeerk let's Jake experience one of his older brother's memories in full. Jake watches the memory of Tom mentally begging the Yeerk to leave his brother alone while the Yeerk pretends to be him trying to convince Jake to join the Sharing. Jake feeling Tom's utter helplessness, misery, and desire for the release of death is bad enough, and then you realize that this is exactly how Tom feels every second of his life.
Tobias realizing that he has to kill an entire alien species for him and the other Animorphs to get home in In the Time of Dinosaurs.
From "The Alien," after Ax meets Cassie's parents, while he's still getting used to his human morph:

Cassie: Yeah, my Dad is going bald. It's normal for humans, but he doesn't like to talk about it.
Ax: I understand. My father's hooves are getting dull. It's normal as well, but he doesn't like to mention it.
Cassie: What are they like, your parents?
Ax: They are very nice. They...
Cassie: They what?
Ax: I seem to have an obstruction in my throat. I am having some difficulty speaking. Is this normal?
Cassie: You miss them. That's normal.

Another Ax moment: after Ax, interacting with his own kind for the first time in a very long time on Leera, puts his faith in them at the expense of his human friends and then discovers that doing so was a big mistake, he has to face his friends again. After a few tense minutes, he admits that he was wrong and tells Jake that from now on, he's the only prince that Ax will follow. The tearjerking part comes when Jake, for the first and only time in their long friendship, doesn't respond with his usual "Don't call me Prince." He just nods.
The Ellimist Chronicles, learning that the enigmatic, cryptic god-figure was once just a geeky, kind-hearted alien teenager - and then watching the process of him losing everything, everything, to become what he is. In the end, there is no one at all on any world in the universe that he's on equal terms with. He's completely alone - except for Crayak, the only one with whom he can play the games he once loved, and whose only desire is to destroy the life that Ellimist creates. He confides and then offers comfort in Rachel's last instants of life:

Did it matter? In the end. My life and my - my death - did it change anything? Did I matter?
Yes. You were brave. You were strong. You were good. You mattered.
Yeah. Okay, then. Okay, then...

David even has a Tear Jerker moment in #48. He might have gone down the wrong path, but if the scene where he accepts his death with dignity and tearfully begs Rachel to end his misery doesn't bring tears to your eyes, what the hell will?

David: It's a beautiful world. I'll miss it.

Ax realizing that Visser Three being a Yeerk must mean that there was an Andalite being enslaved by him once they finally meet in #8. Alloran begging Ax to kill him and having trouble remembering his own name makes you wish that Ax could jut end it then but he's so unprepared for the encounter that he can't.